diff --git a/.Rbuildignore b/.Rbuildignore
index f28ce43bbb10f132a4fba935c9438ec1515e0076..4b009f4ef6e35a1a3e5f00f2ee9d73592dd12220 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -4,4 +4,5 @@
^codecov\.yml$
^appveyor\.yml$
^NEWS\.md$
-^\.git*
\ No newline at end of file
+^\.git*
+^docs$
diff --git a/NEWS.md b/NEWS.md
index 99263acf2807c3bf1a183f3d53bb6a6274313694..27bbf3203470fbb9a0b3afb118952f16c08d2a55 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,48 +1,48 @@
-# 1.1.4
+## Version 1.1.4 (2017-08-04)
* Fix group factors bug
-# 1.1.3
+## Version 1.1.3 (2017-07-20)
* Add verbose option to scDDEstimate
* Change "mean-dropout" to "mean-zeros" in compareSCESets
-# 1.1.2
+## Version 1.1.2 (2017-07-16)
* Update summariseDiff
* Update scDDEstimate, now estimates gene types
* Fix error in lun2Estimate
* Import SummarizedExperiment to avoid warnings
-# 1.1.1
+## Version 1.1.1 (2017-07-07)
* Add batch effects to Splat simulation
* Make Splat group assignment probabilistic
* Update SplatParams with new parameters
-# 1.1.0
+## Version 1.1.0 (2017-07-07)
* Bioconductor 3.6 devel
-# 1.0.3
+## Version 1.0.3 (2017-05-26)
* Update citation
-# 1.0.2
+## Version 1.0.2 (2017-05-15)
* Fix error handling when fitting means
-# 1.0.1
+## Version 1.0.1 (2017-04-28)
* Fix scales in some difference plots
* Fix colours in difference plots
* Fix panel legends
-# 1.0.0
+# Version 1.0.0 (2017-04-28)
* Bioconductor 3.5 release
-# 0.99.15
+## Version 0.99.15 (2017-04-14)
* Add summariseDiff function
* Add BPPARAM argument to scDDSimulate
@@ -50,19 +50,19 @@
* Add limits to zeros diff plots
* Remove estimation of dropout.present
-# 0.99.14
+## Version 0.99.14 (2017-03-28)
* Add functions for making comparison panels
* Add panel section to vignette
* Change variance plot scale (for consistency)
-# 0.99.13
+## Version 0.99.13 (2017-03-25)
* Modify how Lun2Params stores gene paramters to use data.frame
* Move sampling of genes/cells to lun2Simulate
* Return to old Lun2 nGenes estimate
-# 0.99.12
+## Version 0.99.12 (2017-03-22)
* Add diffSCESets function
* Update compareSCESets plots
@@ -70,127 +70,127 @@
* Modify how addFeatureStats names columns
* Add infinte bcv.df warning to splatSimulate
-# 0.99.11
+## Version 0.99.11 (2017-03-20)
* Add parallel option to lun2Estimate
* Allow non-integer library sizes in Lun2Params
* Adjust dropout eta value
* Adjust comparison plots
-# 0.99.10
+## Version 0.99.10 (2017-03-07)
* Improve Splat estimation procedure
* Update default Splat parameters
* Remove out.loProb Splat parameter
* Add MeanZeros plot to compareSCESets
-# 0.99.9
+## Version 0.99.9 (2017-02-02)
* Add addGeneLengths function
* Update scDD reference
-# 0.99.8
+## Version 0.99.8 (2017-01-23)
* Fix bug that meant non-linear path factors weren't stored in output
-# 0.99.7
+## Version 0.99.7 (2017-01-10)
* Small changes to avoid NOTEs and reduce check time
-# 0.99.6
+## Version 0.99.6 (2016-12-29)
* Add installation to vignette
* Add detail about counts matrix to vignette
* Replace 1:x with seq_len/seq_along
-# 0.99.5
+## Version 0.99.5 (2016-12-28)
* Set R_TESTS environment
-# 0.99.4
+## Version 0.99.4 (2016-12-23)
* Version bump to start build
-# splatter 0.99.3
+## Version 0.99.3 (2016-12-21)
* Fix to match Bioconductor version of scDD
* Add logo to repository
-# splatter 0.99.2
+## Version 0.99.2 (2016-12-13)
* Add rownames, colnames to matrices in splatSimulate, lunSimulate
* Bump R version to 3.4
-# splatter 0.99.1
+## Version 0.99.1 (2016-12-12)
* Address Biocondutor build warnings, notes
-# splatter 0.99.0
+# Version 0.99.0 (2016-12-05)
* Submit to Bioconductor
-# splatter 0.12.1
+## Version 0.12.1 (2016-11-25)
* Fix bug in compareSCESets
* Dataset order is now kept in plots
-# splatter 0.12.0
+## Version 0.12.0 (2016-10-25)
* Add compareSCESets function
* Update vignette
* Fix LunParams validity bug
* Add logo
-# splatter 0.11.1
+## Version 0.11.1 (2016-11-23)
* Fix bug in splatSimulatePaths that caused NAs
-# splatter 0.11.0
+## Version 0.11.0 (2016-11-22)
* Make compatible with Bioconductor 3.4
-# splatter 0.10.1
+## Version 0.10.1 (2016-10-17)
* Fix error for SCESets in lun2Estimate, scDDEstimate
-# splatter 0.10.0
+## Version 0.10.0 (2016-10-16)
* Add listSims function
* Add vignette
-# splatter 0.9.0
+## Version 0.9.0 (2016-10-15)
* Add scDD simulation
-# splatter 0.8.0
+## Version 0.8.0 (2016-10-15)
* Add Lun2 simulation
-# splatter 0.7.0
+## Version 0.7.0 (2016-10-14)
* Redesign how parameters are stored
* Each simulation now has it's own S4 Params class
* Modify exisiting simulations to use new parameter objects
-# splatter 0.6.0
+## Version 0.6.0 (2016-10-12)
* Add Lun simulation
* Modify splatParams to take Lun parameters
-# splatter 0.5.0
+## Version 0.5.0 (2016-10-12)
* Add simple simulation
-# splatter 0.4.0
+## Version 0.4.0 (2016-10-12)
* Add splatter simulations
* Modify some parts of splatParams and fix bugs
-# splatter 0.3.0
+## Version 0.3.0 (2016-10-06)
* Added parameter estimation functions
-# splatter 0.2.0
+## Version 0.2.0 (2016-10-06)
* Added splatParams object
* Added functions for interacting with splatParams
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
new file mode 100644
index 0000000000000000000000000000000000000000..a27f1884b89ac3af66eac7414b9f0ffbd8652216
--- /dev/null
+++ b/docs/LICENSE.html
@@ -0,0 +1,786 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>License • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="pkgdown.css" rel="stylesheet">
+<script src="jquery.sticky-kit.min.js"></script>
+<script src="pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-license">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="/index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="contents col-md-12">
+ <div class="page-header">
+ <h1>License</h1>
+ </div>
+
+<pre> GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users. We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+ To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights. Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received. You must make sure that they, too, receive
+or can get the source code. And you must show them these terms so they
+know their rights.
+
+ Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+ For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software. For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+ Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so. This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software. The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable. Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products. If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+ Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary. To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ TERMS AND CONDITIONS
+
+ 0. Definitions.
+
+ "This License" refers to version 3 of the GNU General Public License.
+
+ "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+ "The Program" refers to any copyrightable work licensed under this
+License. Each licensee is addressed as "you". "Licensees" and
+"recipients" may be individuals or organizations.
+
+ To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy. The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+ A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+ To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy. Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+ To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+ An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License. If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+ 1. Source Code.
+
+ The "source code" for a work means the preferred form of the work
+for making modifications to it. "Object code" means any non-source
+form of a work.
+
+ A "Standard Interface" means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that
+is widely used among developers working in that language.
+
+ The "System Libraries" of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that
+Major Component, or to implement a Standard Interface for which an
+implementation is available to the public in source code form. A
+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.
+
+ The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities. However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work. For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+
+ The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+Source.
+
+ The Corresponding Source for a work in source code form is that
+same work.
+
+ 2. Basic Permissions.
+
+ All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met. This License explicitly affirms your unlimited
+permission to run the unmodified Program. The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work. This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+
+ You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force. You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright. Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.
+
+ Conveying under any other circumstances is permitted solely under
+the conditions stated below. Sublicensing is not allowed; section 10
+makes it unnecessary.
+
+ 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+ No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+measures.
+
+ When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.
+
+ 4. Conveying Verbatim Copies.
+
+ You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.
+
+ You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.
+
+ 5. Conveying Modified Source Versions.
+
+ You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:
+
+ a) The work must carry prominent notices stating that you modified
+ it, and giving a relevant date.
+
+ b) The work must carry prominent notices stating that it is
+ released under this License and any conditions added under section
+ 7. This requirement modifies the requirement in section 4 to
+ "keep intact all notices".
+
+ c) You must license the entire work, as a whole, under this
+ License to anyone who comes into possession of a copy. This
+ License will therefore apply, along with any applicable section 7
+ additional terms, to the whole of the work, and all its parts,
+ regardless of how they are packaged. This License gives no
+ permission to license the work in any other way, but it does not
+ invalidate such permission if you have separately received it.
+
+ d) If the work has interactive user interfaces, each must display
+ Appropriate Legal Notices; however, if the Program has interactive
+ interfaces that do not display Appropriate Legal Notices, your
+ work need not make them do so.
+
+ A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work,
+and which are not combined with it such as to form a larger program,
+in or on a volume of a storage or distribution medium, is called an
+"aggregate" if the compilation and its resulting copyright are not
+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.
+
+ 6. Conveying Non-Source Forms.
+
+ You may convey a covered work in object code form under the terms
+of sections 4 and 5, provided that you also convey the
+machine-readable Corresponding Source under the terms of this License,
+in one of these ways:
+
+ a) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by the
+ Corresponding Source fixed on a durable physical medium
+ customarily used for software interchange.
+
+ b) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by a
+ written offer, valid for at least three years and valid for as
+ long as you offer spare parts or customer support for that product
+ model, to give anyone who possesses the object code either (1) a
+ copy of the Corresponding Source for all the software in the
+ product that is covered by this License, on a durable physical
+ medium customarily used for software interchange, for a price no
+ more than your reasonable cost of physically performing this
+ conveying of source, or (2) access to copy the
+ Corresponding Source from a network server at no charge.
+
+ c) Convey individual copies of the object code with a copy of the
+ written offer to provide the Corresponding Source. This
+ alternative is allowed only occasionally and noncommercially, and
+ only if you received the object code with such an offer, in accord
+ with subsection 6b.
+
+ d) Convey the object code by offering access from a designated
+ place (gratis or for a charge), and offer equivalent access to the
+ Corresponding Source in the same way through the same place at no
+ further charge. You need not require recipients to copy the
+ Corresponding Source along with the object code. If the place to
+ copy the object code is a network server, the Corresponding Source
+ may be on a different server (operated by you or a third party)
+ that supports equivalent copying facilities, provided you maintain
+ clear directions next to the object code saying where to find the
+ Corresponding Source. Regardless of what server hosts the
+ Corresponding Source, you remain obligated to ensure that it is
+ available for as long as needed to satisfy these requirements.
+
+ e) Convey the object code using peer-to-peer transmission, provided
+ you inform other peers where the object code and Corresponding
+ Source of the work are being offered to the general public at no
+ charge under subsection 6d.
+
+ A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.
+
+ A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling. In determining whether a product is a consumer product,
+doubtful cases shall be resolved in favor of coverage. For a particular
+product received by a particular user, "normally used" refers to a
+typical or common use of that class of product, regardless of the status
+of the particular user or of the way in which the particular user
+actually uses, or expects or is expected to use, the product. A product
+is a consumer product regardless of whether the product has substantial
+commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.
+
+ "Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from
+a modified version of its Corresponding Source. The information must
+suffice to ensure that the continued functioning of the modified object
+code is in no case prevented or interfered with solely because
+modification has been made.
+
+ If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information. But this requirement does not apply
+if neither you nor any third party retains the ability to install
+modified object code on the User Product (for example, the work has
+been installed in ROM).
+
+ The requirement to provide Installation Information does not include a
+requirement to continue to provide support service, warranty, or updates
+for a work that has been modified or installed by the recipient, or for
+the User Product in which it has been modified or installed. Access to a
+network may be denied when the modification itself materially and
+adversely affects the operation of the network or violates the rules and
+protocols for communication across the network.
+
+ Corresponding Source conveyed, and Installation Information provided,
+in accord with this section must be in a format that is publicly
+documented (and with an implementation available to the public in
+source code form), and must require no special password or key for
+unpacking, reading or copying.
+
+ 7. Additional Terms.
+
+ "Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+ When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
+additional permissions on material, added by you to a covered work,
+for which you have or can give appropriate copyright permission.
+
+ Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
+
+ a) Disclaiming warranty or limiting liability differently from the
+ terms of sections 15 and 16 of this License; or
+
+ b) Requiring preservation of specified reasonable legal notices or
+ author attributions in that material or in the Appropriate Legal
+ Notices displayed by works containing it; or
+
+ c) Prohibiting misrepresentation of the origin of that material, or
+ requiring that modified versions of such material be marked in
+ reasonable ways as different from the original version; or
+
+ d) Limiting the use for publicity purposes of names of licensors or
+ authors of the material; or
+
+ e) Declining to grant rights under trademark law for use of some
+ trade names, trademarks, or service marks; or
+
+ f) Requiring indemnification of licensors and authors of that
+ material by anyone who conveys the material (or modified versions of
+ it) with contractual assumptions of liability to the recipient, for
+ any liability that these contractual assumptions directly impose on
+ those licensors and authors.
+
+ All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term. If a license document contains
+a further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms
+of that license document, provided that the further restriction does
+not survive such relicensing or conveying.
+
+ If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.
+
+ Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
+
+ 8. Termination.
+
+ You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+ However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+ Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+ Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+
+ 10. Automatic Licensing of Downstream Recipients.
+
+ Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.
+
+ An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.
+
+ You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.
+
+ Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+ In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+ If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ {one line to give the program's name and a brief idea of what it does.}
+ Copyright (C) {year} {name of author}
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ {project} Copyright (C) {year} {fullname}
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+</pre>
+
+ </div>
+
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/articles/index.html b/docs/articles/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..5c52266081ac0f79b30243b3217826a4a0617b40
--- /dev/null
+++ b/docs/articles/index.html
@@ -0,0 +1,116 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Articles • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-vignette-index">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="page-header">
+ <h1>Articles <small>version 1.1.4</small></h1>
+</div>
+
+<div class="row">
+ <div class="col-md-9">
+ <div class="section ">
+ <h3>All vignettes</h3>
+ <p class="section-desc"></p>
+
+ <ul>
+ <li><a href="splatter.html">Introduction to Splatter</a></li>
+ </ul>
+ </div>
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/articles/splatter-logo-small.png b/docs/articles/splatter-logo-small.png
new file mode 100644
index 0000000000000000000000000000000000000000..cd78c46e70f630623a5916269309b09f5f438e0b
Binary files /dev/null and b/docs/articles/splatter-logo-small.png differ
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
new file mode 100644
index 0000000000000000000000000000000000000000..97fb64edb67dbef6588666ba69bf2599426517b5
--- /dev/null
+++ b/docs/articles/splatter.html
@@ -0,0 +1,928 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>Introduction to Splatter • splatter</title>
+<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+</head>
+<body>
+ <div class="container template-vignette">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+<li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+<ul class="nav navbar-nav navbar-right">
+<li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+</div>
+<!--/.nav-collapse -->
+ </div>
+<!--/.container -->
+</div>
+<!--/.navbar -->
+
+
+ </header><div class="row">
+ <div class="col-md-9">
+ <div class="page-header toc-ignore">
+ <h1>Introduction to Splatter</h1>
+ <h4 class="author">Luke Zappia</h4>
+
+ <h4 class="date">2017-08-04</h4>
+ </div>
+
+
+
+<div class="contents">
+<div class="figure">
+<img src="splatter-logo-small.png" alt="Splatter logo"><p class="caption">Splatter logo</p>
+</div>
+<p>Welcome to Splatter! Splatter is an R package for the simple simulation of single-cell RNA sequencing data. This vignette gives an overview and introduction to Splatter’s functionality.</p>
+<div id="installation" class="section level1">
+<h1 class="hasAnchor">
+<a href="#installation" class="anchor"></a>Installation</h1>
+<p>Splatter can be installed from Bioconductor:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">source</span>(<span class="st">"https://bioconductor.org/biocLite.R"</span>)
+<span class="kw">biocLite</span>(<span class="st">"splatter"</span>)</code></pre></div>
+<p>To install the most recent development version from Github use:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">biocLite</span>(<span class="st">"Oshlack/splatter"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>,
+ <span class="dt">build_vignettes =</span> <span class="ot">TRUE</span>)</code></pre></div>
+</div>
+<div id="quickstart" class="section level1">
+<h1 class="hasAnchor">
+<a href="#quickstart" class="anchor"></a>Quickstart</h1>
+<p>Assuming you already have a matrix of count data similar to that you wish to simulate there are two simple steps to creating a simulated data set with Splatter. Here is an example using the example dataset in the <code>scater</code> package:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Load package</span>
+<span class="kw">library</span>(splatter)</code></pre></div>
+<pre><code>## Loading required package: scater</code></pre>
+<pre><code>## Loading required package: Biobase</code></pre>
+<pre><code>## Loading required package: BiocGenerics</code></pre>
+<pre><code>## Loading required package: parallel</code></pre>
+<pre><code>##
+## Attaching package: 'BiocGenerics'</code></pre>
+<pre><code>## The following objects are masked from 'package:parallel':
+##
+## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
+## clusterExport, clusterMap, parApply, parCapply, parLapply,
+## parLapplyLB, parRapply, parSapply, parSapplyLB</code></pre>
+<pre><code>## The following objects are masked from 'package:stats':
+##
+## IQR, mad, sd, var, xtabs</code></pre>
+<pre><code>## The following objects are masked from 'package:base':
+##
+## anyDuplicated, append, as.data.frame, cbind, colMeans,
+## colnames, colSums, do.call, duplicated, eval, evalq, Filter,
+## Find, get, grep, grepl, intersect, is.unsorted, lapply,
+## lengths, Map, mapply, match, mget, order, paste, pmax,
+## pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
+## rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
+## tapply, union, unique, unsplit, which, which.max, which.min</code></pre>
+<pre><code>## Welcome to Bioconductor
+##
+## Vignettes contain introductory material; view with
+## 'browseVignettes()'. To cite Bioconductor, see
+## 'citation("Biobase")', and for packages 'citation("pkgname")'.</code></pre>
+<pre><code>## Loading required package: ggplot2</code></pre>
+<pre><code>##
+## Attaching package: 'scater'</code></pre>
+<pre><code>## The following object is masked from 'package:stats':
+##
+## filter</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Load example data</span>
+<span class="kw">data</span>(<span class="st">"sc_example_counts"</span>)
+<span class="co"># Estimate parameters from example data</span>
+params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)
+<span class="co"># Simulate data using estimated parameters</span>
+sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">dropout.present =</span> <span class="ot">FALSE</span>)</code></pre></div>
+<pre><code>## Getting parameters...</code></pre>
+<pre><code>## Creating simulation object...</code></pre>
+<pre><code>## Simulating library sizes...</code></pre>
+<pre><code>## Simulating gene means...</code></pre>
+<pre><code>## Simulating BCV...</code></pre>
+<pre><code>## Simulating counts..</code></pre>
+<pre><code>## Simulating dropout (if needed)...</code></pre>
+<pre><code>## Creating final SCESet...</code></pre>
+<pre><code>## Done!</code></pre>
+<p>These steps will be explained in detail in the following sections but briefly the first step takes a dataset and estimates simulation parameters from it and the second step takes those parameters and simulates a new dataset.</p>
+</div>
+<div id="the-splat-simulation" class="section level1">
+<h1 class="hasAnchor">
+<a href="#the-splat-simulation" class="anchor"></a>The Splat simulation</h1>
+<p>Before we look at how we estimate parameters let’s first look at how Splatter simulates data and what those parameters are. We use the term ‘Splat’ to refer to the Splatter’s own simulation and differentiate it from the package itself. The core of the Splat model is a gamma-Poisson distribution used to generate a gene by cell matrix of counts. Mean expression levels for each gene are simulated from a <a href="https://en.wikipedia.org/wiki/Gamma_distribution">gamma distribution</a> and the Biological Coefficient of Variation is used to enforce a mean-variance trend before counts are simulated from a <a href="https://en.wikipedia.org/wiki/Poisson_distribution">Poisson distribution</a>. Splat also allows you to simulate expression outlier genes (genes with mean expression outside the gamma distribution) and dropout (random knock out of counts based on mean expression). Each cell is given an expected library size (simulated from a log-normal distribution) that makes it easier to match to a given dataset.</p>
+<p>Splat can also simulate differential expression between groups of different types of cells or differentiation paths between different cells types where expression changes in a continuous way. These are described further in the <a href="#simulating-counts">simulating counts</a> section.</p>
+<div id="parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#parameters" class="anchor"></a>Parameters</h2>
+<p>The parameters required for the Splat simulation are briefly described here:</p>
+<ul>
+<li>
+<strong>Global parameters</strong>
+<ul>
+<li>
+<code>nGenes</code> - The number of genes to simulate.</li>
+<li>
+<code>nCells</code> - The number of cells to simulate.</li>
+<li>
+<code>seed</code> - Seed to use for generating random numbers.</li>
+</ul>
+</li>
+<li>
+<strong>Batch parameters</strong>
+<ul>
+<li>
+<code>nBatches</code> - The number of batches to simulate.</li>
+<li>
+<code>batchCells</code> - The number of cells in each batch.</li>
+<li>
+<code>batch.facLoc</code> - Location (meanlog) parameter for the batch effects factor log-normal distribution.</li>
+<li>
+<code>batch.facScale</code> - Scale (sdlog) parameter for the batch effects factor log-normal distribution.</li>
+</ul>
+</li>
+<li>
+<strong>Mean parameters</strong>
+<ul>
+<li>
+<code>mean.shape</code> - Shape parameter for the mean gamma distribution.</li>
+<li>
+<code>mean.rate</code> - Rate parameter for the mean gamma distribution.</li>
+</ul>
+</li>
+<li>
+<strong>Library size parameters</strong>
+<ul>
+<li>
+<code>lib.loc</code> - Location (meanlog) parameter for the library size log-normal distribution.</li>
+<li>
+<code>lib.scale</code> - Scale (sdlog) parameter for the library size log-normal distribution.</li>
+</ul>
+</li>
+<li>
+<strong>Expression outlier parameters</strong>
+<ul>
+<li>
+<code>out.prob</code> - Probability that a gene is an expression outlier.</li>
+<li>
+<code>out.facLoc</code> - Location (meanlog) parameter for the expression outlier factor log-normal distribution.</li>
+<li>
+<code>out.facScale</code> - Scale (sdlog) parameter for the expression outlier factor log-normal distribution.</li>
+</ul>
+</li>
+<li>
+<strong>Group parameters</strong>
+<ul>
+<li>
+<code>nGroups</code> - The number of groups or paths to simulate.</li>
+<li>
+<code>group.prob</code> - The probabilities that cells come from particular groups.</li>
+</ul>
+</li>
+<li>
+<strong>Differential expression parameters</strong>
+<ul>
+<li>
+<code>de.prob</code> - Probability that a gene is differentially expressed in each group or path.</li>
+<li>
+<code>de.loProb</code> - Probability that a differentially expressed gene is down-regulated.</li>
+<li>
+<code>de.facLoc</code> - Location (meanlog) parameter for the differential expression factor log-normal distribution.</li>
+<li>
+<code>de.facScale</code> - Scale (sdlog) parameter for the differential expression factor log-normal distribution.</li>
+</ul>
+</li>
+<li>
+<strong>Biological Coefficient of Variation parameters</strong>
+<ul>
+<li>
+<code>bcv.common</code> - Underlying common dispersion across all genes.</li>
+<li>
+<code>bcv.df</code> - Degrees of Freedom for the BCV inverse chi-squared distribution.</li>
+</ul>
+</li>
+<li>
+<strong>Dropout parameters</strong>
+<ul>
+<li>
+<code>dropout.present</code> - Logical. Whether to simulate dropout.</li>
+<li>
+<code>dropout.mid</code> - Midpoint parameter for the dropout logistic function.</li>
+<li>
+<code>dropout.shape</code> - Shape parameter for the dropout logistic function.</li>
+</ul>
+</li>
+<li>
+<strong>Differentiation path parameters</strong>
+<ul>
+<li>
+<code>path.from</code> - Vector giving the originating point of each path.</li>
+<li>
+<code>path.length</code> - Vector giving the number of steps to simulate along each path.</li>
+<li>
+<code>path.skew</code> - Vector giving the skew of each path.</li>
+<li>
+<code>path.nonlinearProb</code> - Probability that a gene changes expression in a non-linear way along the differentiation path.</li>
+<li>
+<code>path.sigmaFac</code> - Sigma factor for non-linear gene paths.</li>
+</ul>
+</li>
+</ul>
+<p>While this may look like a lot of parameters Splatter attempts to make it easy for the user, both by providing sensible defaults and making it easy to estimate many of the parameters from real data. For more details on the parameters see <code><a href="../reference/SplatParams.html">?SplatParams</a></code>.</p>
+</div>
+</div>
+<div id="the-splatparams-object" class="section level1">
+<h1 class="hasAnchor">
+<a href="#the-splatparams-object" class="anchor"></a>The <code>SplatParams</code> object</h1>
+<p>All the parameters for the Splat simulation are stored in a <code>SplatParams</code> object. Let’s create a new one and see what it looks like.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()
+params</code></pre></div>
+<pre><code>## A Params object of class SplatParams
+## Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+##
+## Global:
+## (Genes) (Cells) [Seed]
+## 10000 100 98513
+##
+## 27 additional parameters
+##
+## Batches:
+## [Batches] [Batch Cells] [Location] [Scale]
+## 1 100 0.1 0.1
+##
+## Mean:
+## (Rate) (Shape)
+## 0.3 0.6
+##
+## Library size:
+## (Location) (Scale)
+## 11 0.2
+##
+## Exprs outliers:
+## (Probability) (Location) (Scale)
+## 0.05 4 0.5
+##
+## Groups:
+## [Groups] [Group Probs]
+## 1 1
+##
+## Diff expr:
+## [Probability] [Down Prob] [Location] [Scale]
+## 0.1 0.5 0.1 0.4
+##
+## BCV:
+## (Common Disp) (DoF)
+## 0.1 60
+##
+## Dropout:
+## [Present] (Midpoint) (Shape)
+## FALSE 0 -1
+##
+## Paths:
+## [From] [Length] [Skew] [Non-linear]
+## 0 100 0.5 0.1
+## [Sigma Factor]
+## 0.8</code></pre>
+<p>As well as telling us what type of object we have (“A <code>Params</code> object of class <code>SplatParams</code>â€) and showing us the values of the parameter this output gives us some extra information. We can see which parameters can be estimated by the <code>splatEstimate</code> function (those in parentheses), which can’t be estimated (those in brackets) and which have been changed from their default values (those in ALL CAPS).</p>
+<div id="getting-and-setting" class="section level2">
+<h2 class="hasAnchor">
+<a href="#getting-and-setting" class="anchor"></a>Getting and setting</h2>
+<p>If we want to look at a particular parameter, for example the number of genes to simulate, we can extract it using the <code>getParam</code> function:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</code></pre></div>
+<pre><code>## [1] 10000</code></pre>
+<p>Alternatively, to give a parameter a new value we can use the <code>setParam</code> function:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)
+<span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</code></pre></div>
+<pre><code>## [1] 5000</code></pre>
+<p>If we want to extract multiple parameters (as a list) or set multiple parameters we can use the <code>getParams</code> or <code>setParams</code> functions:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Set multiple parameters at once (using a list)</span>
+params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">update =</span> <span class="kw">list</span>(<span class="dt">nGenes =</span> <span class="dv">8000</span>, <span class="dt">mean.rate =</span> <span class="fl">0.5</span>))
+<span class="co"># Extract multiple parameters as a list</span>
+<span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"nGenes"</span>, <span class="st">"mean.rate"</span>, <span class="st">"mean.shape"</span>))</code></pre></div>
+<pre><code>## $nGenes
+## [1] 8000
+##
+## $mean.rate
+## [1] 0.5
+##
+## $mean.shape
+## [1] 0.6</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Set multiple parameters at once (using additional arguments)</span>
+params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">mean.shape =</span> <span class="fl">0.5</span>, <span class="dt">de.prob =</span> <span class="fl">0.2</span>)
+params</code></pre></div>
+<pre><code>## A Params object of class SplatParams
+## Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+##
+## Global:
+## (GENES) (Cells) [Seed]
+## 8000 100 98513
+##
+## 27 additional parameters
+##
+## Batches:
+## [Batches] [Batch Cells] [Location] [Scale]
+## 1 100 0.1 0.1
+##
+## Mean:
+## (RATE) (SHAPE)
+## 0.5 0.5
+##
+## Library size:
+## (Location) (Scale)
+## 11 0.2
+##
+## Exprs outliers:
+## (Probability) (Location) (Scale)
+## 0.05 4 0.5
+##
+## Groups:
+## [Groups] [Group Probs]
+## 1 1
+##
+## Diff expr:
+## [PROBABILITY] [Down Prob] [Location] [Scale]
+## 0.2 0.5 0.1 0.4
+##
+## BCV:
+## (Common Disp) (DoF)
+## 0.1 60
+##
+## Dropout:
+## [Present] (Midpoint) (Shape)
+## FALSE 0 -1
+##
+## Paths:
+## [From] [Length] [Skew] [Non-linear]
+## 0 100 0.5 0.1
+## [Sigma Factor]
+## 0.8</code></pre>
+<p>The parameters with have changed are now shown in ALL CAPS to indicate that they been changed form the default.</p>
+<p>We can also set parameters directly when we call <code>newSplatParams</code>:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">lib.loc =</span> <span class="dv">12</span>, <span class="dt">lib.scale =</span> <span class="fl">0.6</span>)
+<span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"lib.loc"</span>, <span class="st">"lib.scale"</span>))</code></pre></div>
+<pre><code>## $lib.loc
+## [1] 12
+##
+## $lib.scale
+## [1] 0.6</code></pre>
+</div>
+</div>
+<div id="estimating-parameters" class="section level1">
+<h1 class="hasAnchor">
+<a href="#estimating-parameters" class="anchor"></a>Estimating parameters</h1>
+<p>Splat allows you to estimate many of it’s parameters from a data set containing counts using the <code>splatEstimate</code> function.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Check that sc_example counts is an integer matrix</span>
+<span class="kw">class</span>(sc_example_counts)</code></pre></div>
+<pre><code>## [1] "matrix"</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">typeof</span>(sc_example_counts)</code></pre></div>
+<pre><code>## [1] "integer"</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span>
+<span class="kw">dim</span>(sc_example_counts)</code></pre></div>
+<pre><code>## [1] 2000 40</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Show the first few entries</span>
+sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
+<pre><code>## Cell_001 Cell_002 Cell_003 Cell_004 Cell_005
+## Gene_0001 0 123 2 0 0
+## Gene_0002 575 65 3 1561 2311
+## Gene_0003 0 0 0 0 1213
+## Gene_0004 0 1 0 0 0
+## Gene_0005 0 0 11 0 0</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</code></pre></div>
+<p>Here we estimated parameters from a counts matrix but <code>splatEstimate</code> can also take an <code>SCESet</code> object from the <code>scater</code> package. The estimation process has the following steps:</p>
+<ol style="list-style-type: decimal">
+<li>Mean parameters are estimated by fitting a gamma distribution to the mean expression levels.</li>
+<li>Library size parameters are estimated by fitting a log-normal distribution to the library sizes.</li>
+<li>Expression outlier parameters are estimated by determining the number of outliers and fitting a log-normal distribution to their difference from the median.</li>
+<li>BCV parameters are estimated using the <code>estimateDisp</code> function from the <code>edgeR</code> package.</li>
+<li>Dropout parameters are estimated by checking if dropout is present and fitting a logistic function to the relationship between mean expression and proportion of zeros.</li>
+</ol>
+<p>For more details of the estimation procedures see <code><a href="../reference/splatEstimate.html">?splatEstimate</a></code>.</p>
+</div>
+<div id="simulating-counts" class="section level1">
+<h1 class="hasAnchor">
+<a href="#simulating-counts" class="anchor"></a>Simulating counts</h1>
+<p>Once we have a set of parameters we are happy with we can use <code>splatSimulate</code> to simulate counts. If we want to make small adjustments to the parameters we can provide them as additional arguments, alternatively if we don’t supply any parameters the defaults will be used:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">dropout.present =</span> <span class="ot">FALSE</span>)</code></pre></div>
+<pre><code>## Getting parameters...</code></pre>
+<pre><code>## Creating simulation object...</code></pre>
+<pre><code>## Simulating library sizes...</code></pre>
+<pre><code>## Simulating gene means...</code></pre>
+<pre><code>## Simulating BCV...</code></pre>
+<pre><code>## Simulating counts..</code></pre>
+<pre><code>## Simulating dropout (if needed)...</code></pre>
+<pre><code>## Creating final SCESet...</code></pre>
+<pre><code>## Done!</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim</code></pre></div>
+<pre><code>## SCESet (storageMode: lockedEnvironment)
+## assayData: 1000 features, 40 samples
+## element names: BaseCellMeans, BatchCellMeans, BCV, CellMeans, counts, exprs, TrueCounts
+## protocolData: none
+## phenoData
+## sampleNames: Cell1 Cell2 ... Cell40 (40 total)
+## varLabels: Cell Batch ExpLibSize
+## varMetadata: labelDescription
+## featureData
+## featureNames: Gene1 Gene2 ... Gene1000 (1000 total)
+## fvarLabels: Gene BaseGeneMean OutlierFactor GeneMean
+## fvarMetadata: labelDescription
+## experimentData: use 'experimentData(object)'
+## Annotation:</code></pre>
+<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is an <code>SCESet</code> object with 1000 features (genes) and 40 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. Additionaly an <code>SCESet</code> contains phenotype information about each cell (accessed using <code>pData</code>) and feature information about each gene (accessed using <code>fData</code>). Splatter uses these slots to store information about the intermediate values of the simulation.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Access the counts</span>
+<span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 71 18 0 0 0
+## Gene2 0 202 97 0 13
+## Gene3 76 0 70 0 4352
+## Gene4 13 0 0 0 0
+## Gene5 563 89 77 0 17</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about genes</span>
+<span class="kw">head</span>(<span class="kw">fData</span>(sim))</code></pre></div>
+<pre><code>## Gene BaseGeneMean OutlierFactor GeneMean
+## Gene1 Gene1 12.15713 1 12.15713
+## Gene2 Gene2 24.31063 1 24.31063
+## Gene3 Gene3 297.25887 1 297.25887
+## Gene4 Gene4 59.50166 1 59.50166
+## Gene5 Gene5 22.53820 1 22.53820
+## Gene6 Gene6 20.61026 1 20.61026</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about cells</span>
+<span class="kw">head</span>(<span class="kw">pData</span>(sim))</code></pre></div>
+<pre><code>## Cell Batch ExpLibSize
+## Cell1 Cell1 Batch1 95909.41
+## Cell2 Cell2 Batch1 244118.47
+## Cell3 Cell3 Batch1 240747.25
+## Cell4 Cell4 Batch1 271459.87
+## Cell5 Cell5 Batch1 424160.08
+## Cell6 Cell6 Batch1 228110.31</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Gene by cell matrices</span>
+<span class="kw">names</span>(<span class="kw">assayData</span>(sim))</code></pre></div>
+<pre><code>## [1] "TrueCounts" "BaseCellMeans" "BatchCellMeans" "counts"
+## [5] "BCV" "CellMeans" "exprs"</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Example of cell means matrix</span>
+<span class="kw">get_exprs</span>(sim, <span class="st">"CellMeans"</span>)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 65.5696590 1.391352e+01 0.06193530 2.453784e-02 1.355897e-03
+## Gene2 0.4790134 2.126821e+02 102.46301607 3.225135e-09 9.960240e+00
+## Gene3 67.4445673 4.695054e-05 71.05222310 6.950506e-11 4.334285e+03
+## Gene4 10.4052334 9.127828e-08 0.01250279 1.721067e-07 1.163755e-16
+## Gene5 556.8580925 8.854150e+01 67.68883291 1.097594e-06 1.449732e+01</code></pre>
+<p>An additional (big) advantage of outputting an <code>SCESet</code> is that we get immediate access to all of the <code>scater</code> functions. For example we can make a PCA plot:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plotPCA</span>(sim)</code></pre></div>
+<p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
+<p>(<strong>NOTE:</strong> Your values and plots may look different as the simulation is random and produces different results each time it is run.)</p>
+<p>For more details of the <code>SCESet</code> and what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
+<p>The <code>splatSimulate</code> function outputs the following additional information about the simulation:</p>
+<ul>
+<li>
+<strong>Cell information (<code>pData</code>)</strong>
+<ul>
+<li>
+<code>Cell</code> - Unique cell identifier.</li>
+<li>
+<code>Group</code> - The group or path the cell belongs to.</li>
+<li>
+<code>ExpLibSize</code> - The expected library size for that cell.</li>
+<li>
+<code>Step</code> (paths only) - How far along the path each cell is.</li>
+</ul>
+</li>
+<li>
+<strong>Gene information (<code>fData</code>)</strong>
+<ul>
+<li>
+<code>Gene</code> - Unique gene identifier.</li>
+<li>
+<code>BaseGeneMean</code> - The base expression level for that gene.</li>
+<li>
+<code>OutlierFactor</code> - Expression outlier factor for that gene (1 is not an outlier).</li>
+<li>
+<code>GeneMean</code> - Expression level after applying outlier factors.</li>
+<li>
+<code>DEFac[Group]</code> - The differential expression factor for each gene in a particular group (1 is not differentially expressed).</li>
+<li>
+<code>GeneMean[Group]</code> - Expression level of a gene in a particular group after applying differential expression factors.</li>
+</ul>
+</li>
+<li>
+<strong>Gene by cell information (<code>assayData</code>)</strong>
+<ul>
+<li>
+<code>BaseCellMeans</code> - The expression of genes in each cell adjusted for expected library size.</li>
+<li>
+<code>BCV</code> - The Biological Coefficient of Variation for each gene in each cell.</li>
+<li>
+<code>CellMeans</code> - The expression level of genes in each cell adjusted for BCV.</li>
+<li>
+<code>TrueCounts</code> - The simulated counts before dropout.</li>
+<li>
+<code>Dropout</code> - Logical matrix showing which counts have been dropped in which cells.</li>
+</ul>
+</li>
+</ul>
+<p>Values that have been added by Splatter are named using <code>UpperCamelCase</code> to separate them from the <code>underscore_naming</code> used by <code>scater</code>. For more information on the simulation see <code><a href="../reference/splatSimulate.html">?splatSimulate</a></code>.</p>
+<div id="simulating-groups" class="section level2">
+<h2 class="hasAnchor">
+<a href="#simulating-groups" class="anchor"></a>Simulating groups</h2>
+<p>So far we have only simulated a single population of cells but often we are interested in investigating a mixed population of cells and looking to see what cell types are present or what differences there are between them. Splatter is able to simulate these situations by changing the <code>method</code> argument Here we are going to simulate two groups, by specifying the <code>group.prob</code> parameter and setting the <code>method</code> parameter to <code>"groups"</code>:</p>
+<p>(<strong>NOTE:</strong> We have also set the <code>verbose</code> argument to <code>FALSE</code> to stop Splatter printing progress messages.)</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,
+ <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
+<span class="kw">plotPCA</span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</code></pre></div>
+<p><img src="splatter_files/figure-html/groups-1.png" width="576" style="display: block; margin: auto;"></p>
+<p>As we have set both the group probabilites to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilites that sum to 1.</p>
+</div>
+<div id="simulating-paths" class="section level2">
+<h2 class="hasAnchor">
+<a href="#simulating-paths" class="anchor"></a>Simulating paths</h2>
+<p>The other situation that is often of interest is a differentiation process where one cell type is changing into another. Splatter approximates this process by simulating a series of steps between two groups and randomly assigning each cell to a step. We can create this kind of simulation using the <code>"paths"</code> method.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.paths <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
+<span class="kw">plotPCA</span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</code></pre></div>
+<p><img src="splatter_files/figure-html/paths-1.png" width="576" style="display: block; margin: auto;"></p>
+<p>Here the colours represent the “step†of each cell or how far along the differentiation path it is. We can see that the cells with dark colours are more similar to the originating cell type and the light coloured cells are closer to the final, differentiated, cell type. By setting additional parameters it is possible to simulate more complex process (for example multiple mature cell types from a single progenitor).</p>
+</div>
+<div id="batch-effects" class="section level2">
+<h2 class="hasAnchor">
+<a href="#batch-effects" class="anchor"></a>Batch effects</h2>
+<p>Another factor that is important in the analysis of any sequencing experiment are batch effects, technical variation that is common to a set of samples processed at the same time. We apply batch effects by telling Splatter how many cells are in each batch:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.batches <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
+<span class="kw">plotPCA</span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</code></pre></div>
+<p><img src="splatter_files/figure-html/batches-1.png" width="576" style="display: block; margin: auto;"></p>
+<p>This looks at lot like when we simulated groups and that is because the process is very similar. The difference is that batch effects are applied to all genes, not just those that are differentially expressed, and the effects are usually smaller. By combining groups and batches we can simulate both unwanted variation that we aren’t interested in (batch) and the wanted variation we are looking for (group):</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),
+ <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
+<span class="kw">plotPCA</span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</code></pre></div>
+<p><img src="splatter_files/figure-html/batch-groups-1.png" width="576" style="display: block; margin: auto;"></p>
+<p>Here we see that the effects of the group (first component) are stronger than the batch effects (second component) but by adjusting the parameters we could made the batch effects dominate.</p>
+</div>
+<div id="convenience-functions" class="section level2">
+<h2 class="hasAnchor">
+<a href="#convenience-functions" class="anchor"></a>Convenience functions</h2>
+<p>Each of the Splatter simulation methods has it’s own convenience function. To simulate a single population use <code><a href="../reference/splatSimulate.html">splatSimulateSingle()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "single")</a></code>), to simulate grops use <code><a href="../reference/splatSimulate.html">splatSimulateGroups()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "groups")</a></code>) or to simulate paths use <code><a href="../reference/splatSimulate.html">splatSimulatePaths()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "paths")</a></code>).</p>
+</div>
+</div>
+<div id="other-simulations" class="section level1">
+<h1 class="hasAnchor">
+<a href="#other-simulations" class="anchor"></a>Other simulations</h1>
+<p>As well as it’s own Splat simulation method the Splatter package contains implementations of other single-cell RNA-seq simulations that have been published or wrappers around simulations included in other packages. To see all the available simulations run the <code><a href="../reference/listSims.html">listSims()</a></code> function:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</code></pre></div>
+<pre><code>## Splatter currently contains 8 simulations
+##
+## Splat (splat)
+## DOI: Github:
+## The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout can be optionally added.
+##
+## Splat Single (splatSingle)
+## DOI: Github:
+## The Splat simulation with a single population.
+##
+## Splat Groups (splatGroups)
+## DOI: Github:
+## The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution.
+##
+## Splat Paths (splatPaths)
+## DOI: Github:
+## The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways.
+##
+## Simple (simple)
+## DOI: Github:
+## A simple simulation with gamma means and negative binomial counts.
+##
+## Lun (lun)
+## DOI: 10.1186/s13059-016-0947-7 Github: MarioniLab/Deconvolution2016
+## Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.
+##
+## Lun 2 (lun2)
+## DOI: 10.1101/073973 Github: MarioniLab/PlateEffects2016
+## Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.
+##
+## scDD (scDD)
+## DOI: 10.1186/s13059-016-1077-y Github: kdkorthauer/scDD
+## The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.</code></pre>
+<p>(or more conveniently for the vignette as a table)</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</code></pre></div>
+<table class="table">
+<thead><tr class="header">
+<th align="left">Name</th>
+<th align="left">Prefix</th>
+<th align="left">DOI</th>
+<th align="left">Github</th>
+<th align="left">Description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="left">Splat</td>
+<td align="left">splat</td>
+<td align="left"></td>
+<td align="left"></td>
+<td align="left">The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout can be optionally added.</td>
+</tr>
+<tr class="even">
+<td align="left">Splat Single</td>
+<td align="left">splatSingle</td>
+<td align="left"></td>
+<td align="left"></td>
+<td align="left">The Splat simulation with a single population.</td>
+</tr>
+<tr class="odd">
+<td align="left">Splat Groups</td>
+<td align="left">splatGroups</td>
+<td align="left"></td>
+<td align="left"></td>
+<td align="left">The Splat simulation with multiple groups. Each group can have it’s own differential expression probability and fold change distribution.</td>
+</tr>
+<tr class="even">
+<td align="left">Splat Paths</td>
+<td align="left">splatPaths</td>
+<td align="left"></td>
+<td align="left"></td>
+<td align="left">The Splat simulation with differentiation paths. Each path can have it’s own length, skew and probability. Genes can change in non-linear ways.</td>
+</tr>
+<tr class="odd">
+<td align="left">Simple</td>
+<td align="left">simple</td>
+<td align="left"></td>
+<td align="left"></td>
+<td align="left">A simple simulation with gamma means and negative binomial counts.</td>
+</tr>
+<tr class="even">
+<td align="left">Lun</td>
+<td align="left">lun</td>
+<td align="left">10.1186/s13059-016-0947-7</td>
+<td align="left">MarioniLab/Deconvolution2016</td>
+<td align="left">Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.</td>
+</tr>
+<tr class="odd">
+<td align="left">Lun 2</td>
+<td align="left">lun2</td>
+<td align="left">10.1101/073973</td>
+<td align="left">MarioniLab/PlateEffects2016</td>
+<td align="left">Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.</td>
+</tr>
+<tr class="even">
+<td align="left">scDD</td>
+<td align="left">scDD</td>
+<td align="left">10.1186/s13059-016-1077-y</td>
+<td align="left">kdkorthauer/scDD</td>
+<td align="left">The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.</td>
+</tr>
+</tbody>
+</table>
+<p>Each simulation has it’s own prefix which gives the name of the functions associated with that simulation. For example the prefix for the simple simulation is <code>simple</code> so it would store it’s parameters in a <code>SimpleParams</code> object that can be created using <code><a href="../reference/newParams.html">newSimpleParams()</a></code> or estimated from real data using <code><a href="../reference/simpleEstimate.html">simpleEstimate()</a></code>. To simulate data using that simulation you would use <code><a href="../reference/simpleSimulate.html">simpleSimulate()</a></code>. Each simulation returns an <code>SCESet</code> object with intermediate values similar to that returned by <code><a href="../reference/splatSimulate.html">splatSimulate()</a></code>. For more detailed information on each simulation see the appropriate help page (eg. <code><a href="../reference/simpleSimulate.html">?simpleSimulate</a></code> for information on how the simple simulation works or <code><a href="../reference/lun2Estimate.html">?lun2Estimate</a></code> for details of how the Lun 2 simulation estimates parameters) or refer to the appropriate paper or package.</p>
+</div>
+<div id="other-expression-values" class="section level1">
+<h1 class="hasAnchor">
+<a href="#other-expression-values" class="anchor"></a>Other expression values</h1>
+<p>Splatter is designed to simulate count data but some analysis methods expect other expression values, particularly length-normalised values such as TPM or FPKM. The <code>scater</code> package has functions for adding these values to an <code>SCESet</code> object but they require a length for each gene. The <code>addGeneLengths</code> can be used to simulate these lengths:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)
+sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)
+<span class="kw">head</span>(<span class="kw">fData</span>(sim))</code></pre></div>
+<pre><code>## Gene GeneMean Length
+## Gene1 Gene1 0.0002067453 1694
+## Gene2 Gene2 0.2420681809 1908
+## Gene3 Gene3 1.1117145796 6058
+## Gene4 Gene4 0.1920623085 15962
+## Gene5 Gene5 0.1872010591 3664
+## Gene6 Gene6 0.2867576121 12947</code></pre>
+<p>We can then use <code>scater</code> to calculate TPM:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw">calculateTPM</span>(sim, <span class="kw">fData</span>(sim)<span class="op">$</span>Length)
+<span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 0.00000 0 0.00000 0.00000 0
+## Gene2 0.00000 0 0.00000 0.00000 0
+## Gene3 53.00124 0 26.08949 53.40399 0
+## Gene4 0.00000 0 0.00000 0.00000 0
+## Gene5 43.81571 0 43.13596 0.00000 0</code></pre>
+<p>The default method used by <code>addGeneLengths</code> to simulate lengths is to generate values from a log-normal distribution which are then rounded to give an integer length. The parameters for this distribution are based on human protein coding genes but can be adjusted if needed (for example for other species). Alternatively lengths can be sampled from a provided vector (see <code><a href="../reference/addGeneLengths.html">?addGeneLengths</a></code> for details and an example).</p>
+</div>
+<div id="comparing-simulations-and-real-data" class="section level1">
+<h1 class="hasAnchor">
+<a href="#comparing-simulations-and-real-data" class="anchor"></a>Comparing simulations and real data</h1>
+<p>One thing you might like to do after simulating data is to compare it to a real dataset, or compare simulations with different parameters or models. Splatter provides a function <code>compareSCESets</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SCESet</code> objects, combines the datasets and produces some plots comparing them. Let’s make two small simulations and see how they compare.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
+sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
+comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCESets.html">compareSCESets</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))
+
+<span class="kw">names</span>(comparison)</code></pre></div>
+<pre><code>## [1] "FeatureData" "PhenoData" "Plots"</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</code></pre></div>
+<pre><code>## [1] "Means" "Variances" "MeanVar" "LibrarySizes"
+## [5] "ZerosGene" "ZerosCell" "MeanZeros"</code></pre>
+<p>The returned list has three items. The first two are the combined datasets by gene (<code>FeatureData</code>) and by cell (<code>PhenoData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</code></pre></div>
+<p><img src="splatter_files/figure-html/comparison-means-1.png" width="576" style="display: block; margin: auto;"></p>
+<p>These are only a few of the plots you might want to consider but it should be easy to make more using the returned data. For example, we could plot the number of expressed genes against the library size:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)
+<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,
+ <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features, <span class="dt">colour =</span> Dataset)) <span class="op">+</span>
+<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>()</code></pre></div>
+<p><img src="splatter_files/figure-html/comparison-libsize-features-1.png" width="576" style="display: block; margin: auto;"></p>
+<div id="comparing-differences" class="section level2">
+<h2 class="hasAnchor">
+<a href="#comparing-differences" class="anchor"></a>Comparing differences</h2>
+<p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCESets</code> function. Similar to <code>compareSCESets</code> this function takes a list of <code>SCESet</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCESets.html">diffSCESets</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)
+difference<span class="op">$</span>Plots<span class="op">$</span>Means</code></pre></div>
+<p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
+<p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</code></pre></div>
+<p><img src="splatter_files/figure-html/difference-qq-1.png" width="576" style="display: block; margin: auto;"></p>
+</div>
+<div id="making-panels" class="section level2">
+<h2 class="hasAnchor">
+<a href="#making-panels" class="anchor"></a>Making panels</h2>
+<p>Each of these comparisons makes several plots which can be a lot to look at. To make this easier, or to produce figures for publications, you can make use of the functions <code>makeCompPanel</code>, <code>makeDiffPanel</code> and <code>makeOverallPanel</code>.</p>
+<p>These functions combine the plots into a single panel using the <code>cowplot</code> package. The panels can be quite large and hard to view (for example in RStudio’s plot viewer) so it can be better to output the panels and view them separately. Luckily <code>cowplot</code> provides a convenient function for saving the images. Here are some suggested parameters for outputting each of the panels:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># This code is just an example and is not run</span>
+panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)
+cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)
+
+panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)
+cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)
+
+panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)
+cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</code></pre></div>
+</div>
+</div>
+<div id="citing-splatter" class="section level1">
+<h1 class="hasAnchor">
+<a href="#citing-splatter" class="anchor"></a>Citing Splatter</h1>
+<p>If you use Splatter in your work please cite our paper:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</code></pre></div>
+<pre><code>##
+## Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of
+## Single-Cell RNA Sequencing Data. bioRxiv. 2017;
+## doi:10.1101/133173
+##
+## A BibTeX entry for LaTeX users is
+##
+## @Article{,
+## author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
+## title = {Splatter: Simulation Of Single-Cell RNA Sequencing Data},
+## journal = {bioRxiv},
+## year = {2017},
+## url = {http://dx.doi.org/10.1101/133173},
+## doi = {10.1101/133173},
+## }</code></pre>
+</div>
+<div id="session-information" class="section level1 unnumbered">
+<h1 class="hasAnchor">
+<a href="#session-information" class="anchor"></a>Session information</h1>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">sessionInfo</span>()</code></pre></div>
+<pre><code>## R version 3.4.1 (2017-06-30)
+## Platform: x86_64-apple-darwin15.6.0 (64-bit)
+## Running under: macOS Sierra 10.12.5
+##
+## Matrix products: default
+## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
+## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
+##
+## locale:
+## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
+##
+## attached base packages:
+## [1] parallel stats graphics grDevices utils datasets methods
+## [8] base
+##
+## other attached packages:
+## [1] splatter_1.1.4 scater_1.4.0 ggplot2_2.2.1
+## [4] Biobase_2.36.2 BiocGenerics_0.22.0
+##
+## loaded via a namespace (and not attached):
+## [1] viridis_0.4.0 edgeR_3.18.1
+## [3] splines_3.4.1 bit64_0.9-7
+## [5] viridisLite_0.2.0 shiny_1.0.3
+## [7] assertthat_0.2.0 highr_0.6
+## [9] sp_1.2-5 stats4_3.4.1
+## [11] blob_1.1.0 GenomeInfoDbData_0.99.0
+## [13] vipor_0.4.5 yaml_2.1.14
+## [15] RSQLite_2.0 backports_1.1.0
+## [17] lattice_0.20-35 glue_1.1.1
+## [19] limma_3.32.4 digest_0.6.12
+## [21] XVector_0.16.0 GenomicRanges_1.28.4
+## [23] checkmate_1.8.3 colorspace_1.3-2
+## [25] cowplot_0.7.0 htmltools_0.3.6
+## [27] httpuv_1.3.5 Matrix_1.2-10
+## [29] plyr_1.8.4 XML_3.98-1.9
+## [31] pkgconfig_2.0.1 biomaRt_2.32.1
+## [33] zlibbioc_1.22.0 xtable_1.8-2
+## [35] scales_0.4.1 BiocParallel_1.10.1
+## [37] tibble_1.3.3 IRanges_2.10.2
+## [39] SummarizedExperiment_1.6.3 lazyeval_0.2.0
+## [41] survival_2.41-3 magrittr_1.5
+## [43] mime_0.5 memoise_1.1.0
+## [45] evaluate_0.10.1 MASS_7.3-47
+## [47] beeswarm_0.2.3 shinydashboard_0.6.1
+## [49] fitdistrplus_1.0-9 tools_3.4.1
+## [51] data.table_1.10.4 matrixStats_0.52.2
+## [53] stringr_1.2.0 S4Vectors_0.14.3
+## [55] munsell_0.4.3 locfit_1.5-9.1
+## [57] DelayedArray_0.2.7 AnnotationDbi_1.38.1
+## [59] bindrcpp_0.2 akima_0.6-2
+## [61] compiler_3.4.1 GenomeInfoDb_1.12.2
+## [63] rlang_0.1.1.9000 rhdf5_2.20.0
+## [65] grid_3.4.1 RCurl_1.95-4.8
+## [67] tximport_1.4.0 rjson_0.2.15
+## [69] labeling_0.3 bitops_1.0-6
+## [71] rmarkdown_1.6 gtable_0.2.0
+## [73] DBI_0.7 reshape2_1.4.2
+## [75] R6_2.2.2 gridExtra_2.2.1
+## [77] knitr_1.16 dplyr_0.7.2
+## [79] bit_1.1-12 bindr_0.1
+## [81] rprojroot_1.2 stringi_1.1.5
+## [83] ggbeeswarm_0.5.3 Rcpp_0.12.12</code></pre>
+</div>
+</div>
+ </div>
+
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <div id="tocnav">
+ <h2 class="hasAnchor">
+<a href="#tocnav" class="anchor"></a>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+<li><a href="#installation">Installation</a></li>
+ <li><a href="#quickstart">Quickstart</a></li>
+ <li>
+<a href="#the-splat-simulation">The Splat simulation</a><ul class="nav nav-pills nav-stacked">
+<li><a href="#parameters">Parameters</a></li>
+ </ul>
+</li>
+ <li>
+<a href="#the-splatparams-object">The <code>SplatParams</code> object</a><ul class="nav nav-pills nav-stacked">
+<li><a href="#getting-and-setting">Getting and setting</a></li>
+ </ul>
+</li>
+ <li><a href="#estimating-parameters">Estimating parameters</a></li>
+ <li>
+<a href="#simulating-counts">Simulating counts</a><ul class="nav nav-pills nav-stacked">
+<li><a href="#simulating-groups">Simulating groups</a></li>
+ <li><a href="#simulating-paths">Simulating paths</a></li>
+ <li><a href="#batch-effects">Batch effects</a></li>
+ <li><a href="#convenience-functions">Convenience functions</a></li>
+ </ul>
+</li>
+ <li><a href="#other-simulations">Other simulations</a></li>
+ <li><a href="#other-expression-values">Other expression values</a></li>
+ <li>
+<a href="#comparing-simulations-and-real-data">Comparing simulations and real data</a><ul class="nav nav-pills nav-stacked">
+<li><a href="#comparing-differences">Comparing differences</a></li>
+ <li><a href="#making-panels">Making panels</a></li>
+ </ul>
+</li>
+ <li><a href="#citing-splatter">Citing Splatter</a></li>
+ <li><a href="#session-information">Session information</a></li>
+ </ul>
+</div>
+ </div>
+
+</div>
+
+
+ <footer><div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+</div>
+
+ </body>
+</html>
diff --git a/docs/articles/splatter_files/figure-html/batch-groups-1.png b/docs/articles/splatter_files/figure-html/batch-groups-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..e557606c542e0f52547b26d0e88c9eded30f90ec
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/batch-groups-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/batches-1.png b/docs/articles/splatter_files/figure-html/batches-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..718d10decb1983163dc2065e8a008e6db8ac1a8d
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/batches-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/comparison-libsize-features-1.png b/docs/articles/splatter_files/figure-html/comparison-libsize-features-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..430a0c83ac850cd7b0a0c10d8210405bc8f6f58c
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/comparison-libsize-features-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/comparison-means-1.png b/docs/articles/splatter_files/figure-html/comparison-means-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..33713811bc6087e6705852520145fc1e54f39141
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/comparison-means-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/difference-1.png b/docs/articles/splatter_files/figure-html/difference-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..0e35a3d035be67d1a57ae6ee3a74e5a9164d83c2
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/difference-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/difference-qq-1.png b/docs/articles/splatter_files/figure-html/difference-qq-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..a68f8138376c01d57b408848e3c8f7f253c86a7d
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/difference-qq-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/groups-1.png b/docs/articles/splatter_files/figure-html/groups-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..cf58b6db7a0befa4964e9ed3c573dba712de8e51
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/groups-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/paths-1.png b/docs/articles/splatter_files/figure-html/paths-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..629246216c858aad23c21d244956b1231f41a358
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/paths-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/pca-1.png b/docs/articles/splatter_files/figure-html/pca-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..a6dd1b43a30c114a4a1a7245cbf528ed29e9f389
Binary files /dev/null and b/docs/articles/splatter_files/figure-html/pca-1.png differ
diff --git a/docs/authors.html b/docs/authors.html
new file mode 100644
index 0000000000000000000000000000000000000000..b34fd647a5e7c57e37fcadf669ff7e2a66140c86
--- /dev/null
+++ b/docs/authors.html
@@ -0,0 +1,143 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Citation and Authors • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="pkgdown.css" rel="stylesheet">
+<script src="jquery.sticky-kit.min.js"></script>
+<script src="pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-citation-authors">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="/index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="contents col-md-9">
+
+ <div class="page-header">
+ <h1>Citation</h1>
+ </div>
+
+ <p>Zappia L, Phipson B and Oshlack A (2017).
+“Splatter: Simulation Of Single-Cell RNA Sequencing Data.”
+<em>bioRxiv</em>.
+doi: <a href="http://doi.org/10.1101/133173">10.1101/133173</a>, <a href="http://dx.doi.org/10.1101/133173">http://dx.doi.org/10.1101/133173</a>.
+</p>
+ <pre>@Article{,
+ author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
+ title = {Splatter: Simulation Of Single-Cell RNA Sequencing Data},
+ journal = {bioRxiv},
+ year = {2017},
+ url = {http://dx.doi.org/10.1101/133173},
+ doi = {10.1101/133173},
+}</pre>
+ <div class="page-header">
+ <h1>Authors</h1>
+ </div>
+
+ <ul class="list-unstyled">
+ <li>
+ <p><strong>Luke Zappia</strong>. Author, maintainer.
+ </p>
+ </li>
+ <li>
+ <p><strong>Belinda Phipson</strong>. Author.
+ </p>
+ </li>
+ <li>
+ <p><strong>Alicia Oshlack</strong>. Author.
+ </p>
+ </li>
+ </ul>
+
+ </div>
+
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/index.html b/docs/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..8f4b8201ab285f65c1585dffde6a17efb4ba919e
--- /dev/null
+++ b/docs/index.html
@@ -0,0 +1,161 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>Simple Simulation of Single-cell RNA Sequencing Data • splatter</title>
+<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+</head>
+<body>
+ <div class="container template-home">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+<li>
+ <a href="/index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="news/index.html">News</a>
+</li>
+ </ul>
+<ul class="nav navbar-nav navbar-right">
+<li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+</div>
+<!--/.nav-collapse -->
+ </div>
+<!--/.container -->
+</div>
+<!--/.navbar -->
+
+
+ </header><div class="row">
+ <div class="contents col-md-9">
+ <div id="splatter" class="section level1">
+<div class="page-header"><h1 class="hasAnchor">
+<a href="#splatter" class="anchor"></a>Splatter</h1></div>
+
+<p><img src="https://s16.postimg.org/xc6u52b0l/splatter_logo_small.png" alt="Splatter logo"></p>
+<p>Splatter is an R package for the simple simulation of single-cell RNA sequencing data. Splatter provides a common interface to multiple simulations that have:</p>
+<ul>
+<li>Functions for estimating simulation parameters</li>
+<li>Objects for storing those parameters</li>
+<li>Functions for simulating counts using those parameters</li>
+</ul>
+<p>Splatter is built on top of <a href="https://github.com/davismcc/scater"><code>scater</code></a> and stores simulations in <code>SCESet</code> objects. Splatter also has functions for comparing simulations and real datasets.</p>
+<div id="installation-" class="section level2">
+<h2 class="hasAnchor">
+<a href="#installation-" class="anchor"></a>Installation.</h2>
+<div id="development-version" class="section level3">
+<h3 class="hasAnchor">
+<a href="#development-version" class="anchor"></a>Development version</h3>
+<p>Splatter has been accepted into the latest version of <a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html">Bioconductor</a> and hence requires the latest version of R (>=3.4).</p>
+<p>If you have these installed Splatter can be installed from Bioconductor using <code>biocLite</code>:</p>
+<pre class="{r}"><code>source("https://bioconductor.org/biocLite.R")
+biocLite("splatter")</code></pre>
+<p>If you wish to build a local version of the vignette use:</p>
+<pre class="{r}"><code>biocLite("splatter", build_vignettes=TRUE)</code></pre>
+<p>This will also build the vignette and install all suggested dependencies (which aren’t required for core functionality). Building the vignette may sometimes fail when run from the command line, if this happens try running the install command in RStudio.</p>
+</div>
+</div>
+<div id="getting-started" class="section level2">
+<h2 class="hasAnchor">
+<a href="#getting-started" class="anchor"></a>Getting started</h2>
+<p>Once installed the best place to get started is the vignette. For most users the most convient way to access this is online <a href="https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html">here</a>.</p>
+<p>Alternatively, if you chose to build the vignette, you can load Splatter, then browse the vignettes:</p>
+<pre class="{r}"><code>library(splatter)
+browseVignettes("splatter")</code></pre>
+<p>This is a detailed document that introduces the main features of Splatter.</p>
+</div>
+<div id="citing-splatter" class="section level2">
+<h2 class="hasAnchor">
+<a href="#citing-splatter" class="anchor"></a>Citing Splatter</h2>
+<p>If you use Splatter please cite our paper <a href="http://dx.doi.org/10.1101/133173">“Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA Sequencing Data. bioRxiv. 2017; doi:10.1101/133173â€</a>.</p>
+<pre><code>@Article{,
+ author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
+ title = {Splatter: Simulation Of Single-Cell RNA Sequencing Data},
+ journal = {bioRxiv},
+ year = {2017},
+ url = {http://dx.doi.org/10.1101/133173},
+ doi = {10.1101/133173},
+ }</code></pre>
+</div>
+</div>
+ </div>
+
+ <div class="col-md-3" id="sidebar">
+ <h2>Links</h2>
+<ul class="list-unstyled">
+<li>Download from BIOC at <br><a href="https://www.bioconductor.org/packages/splatter">https://​www.bioconductor.org/​packages/​splatter</a>
+</li>
+<li>Browse source code at <br><a href="https://github.com/Oshlack/splatter">https://​github.com/​Oshlack/​splatter</a>
+</li>
+<li>Report a bug at <br><a href="https://github.com/Oshlack/splatter/issues">https://​github.com/​Oshlack/​splatter/​issues</a>
+</li>
+</ul>
+<h2>License</h2>
+<p><a href="https://www.r-project.org/Licenses/GPL-3">GPL-3</a> + file <a href="LICENSE.html">LICENSE</a></p>
+<h2>Citation</h2>
+<ul class="list-unstyled">
+<li><a href="authors.html">Citing splatter</a></li>
+</ul>
+<h2>Developers</h2>
+<ul class="list-unstyled">
+<li>Luke Zappia <br><small class="roles"> Author, maintainer </small> </li>
+<li>Belinda Phipson <br><small class="roles"> Author </small> </li>
+<li>Alicia Oshlack <br><small class="roles"> Author </small> </li>
+</ul>
+<h2>Dev status</h2>
+<ul class="list-unstyled">
+<li><a href="https://travis-ci.org/Oshlack/splatter"><img src="https://travis-ci.org/Oshlack/splatter.svg?branch=master" alt="Travis-CI Build Status"></a></li>
+<li><a href="https://codecov.io/github/Oshlack/splatter?branch=master"><img src="https://img.shields.io/codecov/c/github/Oshlack/splatter/master.svg" alt="Coverage Status"></a></li>
+<li><a href="https://ci.appveyor.com/project/Oshlack/splatter"><img src="https://ci.appveyor.com/api/projects/status/github/Oshlack/splatter?branch=master&svg=true" alt="AppVeyor Build Status"></a></li>
+</ul>
+</div>
+</div>
+
+
+ <footer><div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+</div>
+
+ </body>
+</html>
diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js
new file mode 100644
index 0000000000000000000000000000000000000000..e2a3c6de9e8e3b01b04cbbcdb5a2f8e113391de4
--- /dev/null
+++ b/docs/jquery.sticky-kit.min.js
@@ -0,0 +1,9 @@
+/*
+ Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net
+*/
+(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k));
+if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("<div />"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q,
+u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),e<F&&(m=!1,c=q,null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),
+h.detach()),b={position:"",width:"",top:""},a.css(b).removeClass(t).trigger("sticky_kit:unstick")),B&&(b=f.height(),u+q>b&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}),
+a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize",
+y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n<K;n++)d=this[n],J(b(d));return this}}).call(this);
diff --git a/docs/link.svg b/docs/link.svg
new file mode 100644
index 0000000000000000000000000000000000000000..88ad82769b87f10725c57dca6fcf41b4bffe462c
--- /dev/null
+++ b/docs/link.svg
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 19.2.1, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+ viewBox="0 0 20 20" style="enable-background:new 0 0 20 20;" xml:space="preserve">
+<style type="text/css">
+ .st0{fill:#75AADB;}
+</style>
+<path class="st0" d="M4,11.3h1.3v1.3H4c-2,0-4-2.3-4-4.7s2.1-4.7,4-4.7h5.3c1.9,0,4,2.3,4,4.7c0,1.9-1.2,3.6-2.7,4.3v-1.5
+ C11.4,10.2,12,9.1,12,8c0-1.7-1.4-3.3-2.7-3.3H4C2.7,4.7,1.3,6.3,1.3,8S2.7,11.3,4,11.3z M16,7.3h-1.3v1.3H16c1.3,0,2.7,1.6,2.7,3.3
+ s-1.4,3.3-2.7,3.3h-5.3C9.4,15.3,8,13.7,8,12c0-1.1,0.6-2.2,1.3-2.8V7.7C7.9,8.4,6.7,10.1,6.7,12c0,2.4,2.1,4.7,4,4.7H16
+ c1.9,0,4-2.3,4-4.7S18,7.3,16,7.3z"/>
+</svg>
diff --git a/docs/news/index.html b/docs/news/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..c216f5a00d142b5899a576cb8c4749f82fd2ca51
--- /dev/null
+++ b/docs/news/index.html
@@ -0,0 +1,444 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>All news • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-news">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+
+ <div class="col-md-9">
+ <div class="page-header">
+ <h1>Change log <small>All releases</small></h1>
+ </div>
+
+ <div class="contents">
+ <div id="version-1-1-4-2017-08-04" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-4-2017-08-04" class="anchor"></a>Version 1.1.4 (2017-08-04)</h2>
+<ul>
+<li>Fix group factors bug</li>
+</ul>
+</div>
+ <div id="version-1-1-3-2017-07-20" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-3-2017-07-20" class="anchor"></a>Version 1.1.3 (2017-07-20)</h2>
+<ul>
+<li>Add verbose option to scDDEstimate</li>
+<li>Change “mean-dropout†to “mean-zeros†in compareSCESets</li>
+</ul>
+</div>
+ <div id="version-1-1-2-2017-07-16" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-2-2017-07-16" class="anchor"></a>Version 1.1.2 (2017-07-16)</h2>
+<ul>
+<li>Update summariseDiff</li>
+<li>Update scDDEstimate, now estimates gene types</li>
+<li>Fix error in lun2Estimate</li>
+<li>Import SummarizedExperiment to avoid warnings</li>
+</ul>
+</div>
+ <div id="version-1-1-1-2017-07-07" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-1-2017-07-07" class="anchor"></a>Version 1.1.1 (2017-07-07)</h2>
+<ul>
+<li>Add batch effects to Splat simulation</li>
+<li>Make Splat group assignment probabilistic</li>
+<li>Update SplatParams with new parameters</li>
+</ul>
+</div>
+ <div id="version-1-1-0-2017-07-07" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-0-2017-07-07" class="anchor"></a>Version 1.1.0 (2017-07-07)</h2>
+<ul>
+<li>Bioconductor 3.6 devel</li>
+</ul>
+</div>
+ <div id="version-1-0-3-2017-05-26" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-0-3-2017-05-26" class="anchor"></a>Version 1.0.3 (2017-05-26)</h2>
+<ul>
+<li>Update citation</li>
+</ul>
+</div>
+ <div id="version-1-0-2-2017-05-15" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-0-2-2017-05-15" class="anchor"></a>Version 1.0.2 (2017-05-15)</h2>
+<ul>
+<li>Fix error handling when fitting means</li>
+</ul>
+</div>
+ <div id="version-1-0-1-2017-04-28" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-0-1-2017-04-28" class="anchor"></a>Version 1.0.1 (2017-04-28)</h2>
+<ul>
+<li>Fix scales in some difference plots</li>
+<li>Fix colours in difference plots</li>
+<li>Fix panel legends</li>
+</ul>
+</div>
+ <div id="version-1-0-0-2017-04-28" class="section level1">
+<h1 class="hasAnchor">
+<a href="#version-1-0-0-2017-04-28" class="anchor"></a>Version 1.0.0 (2017-04-28)</h1>
+<ul>
+<li>Bioconductor 3.5 release</li>
+</ul>
+<div id="version-0-99-15-2017-04-14" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-15-2017-04-14" class="anchor"></a>Version 0.99.15 (2017-04-14)</h2>
+<ul>
+<li>Add summariseDiff function</li>
+<li>Add BPPARAM argument to scDDSimulate</li>
+<li>Adjust default Splat DE factor parameters</li>
+<li>Add limits to zeros diff plots</li>
+<li>Remove estimation of dropout.present</li>
+</ul>
+</div>
+<div id="version-0-99-14-2017-03-28" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-14-2017-03-28" class="anchor"></a>Version 0.99.14 (2017-03-28)</h2>
+<ul>
+<li>Add functions for making comparison panels</li>
+<li>Add panel section to vignette</li>
+<li>Change variance plot scale (for consistency)</li>
+</ul>
+</div>
+<div id="version-0-99-13-2017-03-25" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-13-2017-03-25" class="anchor"></a>Version 0.99.13 (2017-03-25)</h2>
+<ul>
+<li>Modify how Lun2Params stores gene paramters to use data.frame</li>
+<li>Move sampling of genes/cells to lun2Simulate</li>
+<li>Return to old Lun2 nGenes estimate</li>
+</ul>
+</div>
+<div id="version-0-99-12-2017-03-22" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-12-2017-03-22" class="anchor"></a>Version 0.99.12 (2017-03-22)</h2>
+<ul>
+<li>Add diffSCESets function</li>
+<li>Update compareSCESets plots</li>
+<li>Modify Lun2 nGenes estimate</li>
+<li>Modify how addFeatureStats names columns</li>
+<li>Add infinte bcv.df warning to splatSimulate</li>
+</ul>
+</div>
+<div id="version-0-99-11-2017-03-20" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-11-2017-03-20" class="anchor"></a>Version 0.99.11 (2017-03-20)</h2>
+<ul>
+<li>Add parallel option to lun2Estimate</li>
+<li>Allow non-integer library sizes in Lun2Params</li>
+<li>Adjust dropout eta value</li>
+<li>Adjust comparison plots</li>
+</ul>
+</div>
+<div id="version-0-99-10-2017-03-07" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-10-2017-03-07" class="anchor"></a>Version 0.99.10 (2017-03-07)</h2>
+<ul>
+<li>Improve Splat estimation procedure</li>
+<li>Update default Splat parameters</li>
+<li>Remove out.loProb Splat parameter</li>
+<li>Add MeanZeros plot to compareSCESets</li>
+</ul>
+</div>
+<div id="version-0-99-9-2017-02-02" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-9-2017-02-02" class="anchor"></a>Version 0.99.9 (2017-02-02)</h2>
+<ul>
+<li>Add addGeneLengths function</li>
+<li>Update scDD reference</li>
+</ul>
+</div>
+<div id="version-0-99-8-2017-01-23" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-8-2017-01-23" class="anchor"></a>Version 0.99.8 (2017-01-23)</h2>
+<ul>
+<li>Fix bug that meant non-linear path factors weren’t stored in output</li>
+</ul>
+</div>
+<div id="version-0-99-7-2017-01-10" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-7-2017-01-10" class="anchor"></a>Version 0.99.7 (2017-01-10)</h2>
+<ul>
+<li>Small changes to avoid NOTEs and reduce check time</li>
+</ul>
+</div>
+<div id="version-0-99-6-2016-12-29" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-6-2016-12-29" class="anchor"></a>Version 0.99.6 (2016-12-29)</h2>
+<ul>
+<li>Add installation to vignette</li>
+<li>Add detail about counts matrix to vignette</li>
+<li>Replace 1:x with seq_len/seq_along</li>
+</ul>
+</div>
+<div id="version-0-99-5-2016-12-28" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-5-2016-12-28" class="anchor"></a>Version 0.99.5 (2016-12-28)</h2>
+<ul>
+<li>Set R_TESTS environment</li>
+</ul>
+</div>
+<div id="version-0-99-4-2016-12-23" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-4-2016-12-23" class="anchor"></a>Version 0.99.4 (2016-12-23)</h2>
+<ul>
+<li>Version bump to start build</li>
+</ul>
+</div>
+<div id="version-0-99-3-2016-12-21" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-3-2016-12-21" class="anchor"></a>Version 0.99.3 (2016-12-21)</h2>
+<ul>
+<li>Fix to match Bioconductor version of scDD</li>
+<li>Add logo to repository</li>
+</ul>
+</div>
+<div id="version-0-99-2-2016-12-13" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-2-2016-12-13" class="anchor"></a>Version 0.99.2 (2016-12-13)</h2>
+<ul>
+<li>Add rownames, colnames to matrices in splatSimulate, lunSimulate</li>
+<li>Bump R version to 3.4</li>
+</ul>
+</div>
+<div id="version-0-99-1-2016-12-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-99-1-2016-12-12" class="anchor"></a>Version 0.99.1 (2016-12-12)</h2>
+<ul>
+<li>Address Biocondutor build warnings, notes</li>
+</ul>
+</div>
+</div>
+ <div id="version-0-99-0-2016-12-05" class="section level1">
+<h1 class="hasAnchor">
+<a href="#version-0-99-0-2016-12-05" class="anchor"></a>Version 0.99.0 (2016-12-05)</h1>
+<ul>
+<li>Submit to Bioconductor</li>
+</ul>
+<div id="version-0-12-1-2016-11-25" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-12-1-2016-11-25" class="anchor"></a>Version 0.12.1 (2016-11-25)</h2>
+<ul>
+<li>Fix bug in compareSCESets</li>
+<li>Dataset order is now kept in plots</li>
+</ul>
+</div>
+<div id="version-0-12-0-2016-10-25" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-12-0-2016-10-25" class="anchor"></a>Version 0.12.0 (2016-10-25)</h2>
+<ul>
+<li>Add compareSCESets function</li>
+<li>Update vignette</li>
+<li>Fix LunParams validity bug</li>
+<li>Add logo</li>
+</ul>
+</div>
+<div id="version-0-11-1-2016-11-23" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-11-1-2016-11-23" class="anchor"></a>Version 0.11.1 (2016-11-23)</h2>
+<ul>
+<li>Fix bug in splatSimulatePaths that caused NAs</li>
+</ul>
+</div>
+<div id="version-0-11-0-2016-11-22" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-11-0-2016-11-22" class="anchor"></a>Version 0.11.0 (2016-11-22)</h2>
+<ul>
+<li>Make compatible with Bioconductor 3.4</li>
+</ul>
+</div>
+<div id="version-0-10-1-2016-10-17" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-10-1-2016-10-17" class="anchor"></a>Version 0.10.1 (2016-10-17)</h2>
+<ul>
+<li>Fix error for SCESets in lun2Estimate, scDDEstimate</li>
+</ul>
+</div>
+<div id="version-0-10-0-2016-10-16" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-10-0-2016-10-16" class="anchor"></a>Version 0.10.0 (2016-10-16)</h2>
+<ul>
+<li>Add listSims function</li>
+<li>Add vignette</li>
+</ul>
+</div>
+<div id="version-0-9-0-2016-10-15" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-9-0-2016-10-15" class="anchor"></a>Version 0.9.0 (2016-10-15)</h2>
+<ul>
+<li>Add scDD simulation</li>
+</ul>
+</div>
+<div id="version-0-8-0-2016-10-15" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-8-0-2016-10-15" class="anchor"></a>Version 0.8.0 (2016-10-15)</h2>
+<ul>
+<li>Add Lun2 simulation</li>
+</ul>
+</div>
+<div id="version-0-7-0-2016-10-14" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-7-0-2016-10-14" class="anchor"></a>Version 0.7.0 (2016-10-14)</h2>
+<ul>
+<li>Redesign how parameters are stored</li>
+<li>Each simulation now has it’s own S4 Params class</li>
+<li>Modify exisiting simulations to use new parameter objects</li>
+</ul>
+</div>
+<div id="version-0-6-0-2016-10-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-6-0-2016-10-12" class="anchor"></a>Version 0.6.0 (2016-10-12)</h2>
+<ul>
+<li>Add Lun simulation</li>
+<li>Modify splatParams to take Lun parameters</li>
+</ul>
+</div>
+<div id="version-0-5-0-2016-10-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-5-0-2016-10-12" class="anchor"></a>Version 0.5.0 (2016-10-12)</h2>
+<ul>
+<li>Add simple simulation</li>
+</ul>
+</div>
+<div id="version-0-4-0-2016-10-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-4-0-2016-10-12" class="anchor"></a>Version 0.4.0 (2016-10-12)</h2>
+<ul>
+<li>Add splatter simulations</li>
+<li>Modify some parts of splatParams and fix bugs</li>
+</ul>
+</div>
+<div id="version-0-3-0-2016-10-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-3-0-2016-10-06" class="anchor"></a>Version 0.3.0 (2016-10-06)</h2>
+<ul>
+<li>Added parameter estimation functions</li>
+</ul>
+</div>
+<div id="version-0-2-0-2016-10-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-0-2-0-2016-10-06" class="anchor"></a>Version 0.2.0 (2016-10-06)</h2>
+<ul>
+<li>Added splatParams object</li>
+<li>Added functions for interacting with splatParams</li>
+</ul>
+</div>
+</div>
+ </div>
+ </div>
+
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <div id="tocnav">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#version-1-1-4-2017-08-04">1.1.4</a></li>
+ <li><a href="#version-1-1-3-2017-07-20">1.1.3</a></li>
+ <li><a href="#version-1-1-2-2017-07-16">1.1.2</a></li>
+ <li><a href="#version-1-1-1-2017-07-07">1.1.1</a></li>
+ <li><a href="#version-1-1-0-2017-07-07">1.1.0</a></li>
+ <li><a href="#version-1-0-3-2017-05-26">1.0.3</a></li>
+ <li><a href="#version-1-0-2-2017-05-15">1.0.2</a></li>
+ <li><a href="#version-1-0-1-2017-04-28">1.0.1</a></li>
+ <li><a href="#version-1-0-0-2017-04-28">1.0.0</a></li>
+ <li><a href="#version-0-99-0-2016-12-05">0.99.0</a></li>
+ </ul>
+ </div>
+ </div>
+
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
new file mode 100644
index 0000000000000000000000000000000000000000..209ce57febdc449e03d16b5b0d9323cd33692873
--- /dev/null
+++ b/docs/pkgdown.css
@@ -0,0 +1,163 @@
+/* Sticker footer */
+body > .container {
+ display: flex;
+ padding-top: 60px;
+ min-height: calc(100vh);
+ flex-direction: column;
+}
+
+body > .container .row {
+ flex: 1;
+}
+
+footer {
+ margin-top: 45px;
+ padding: 35px 0 36px;
+ border-top: 1px solid #e5e5e5;
+ color: #666;
+ display: flex;
+}
+footer p {
+ margin-bottom: 0;
+}
+footer div {
+ flex: 1;
+}
+footer .pkgdown {
+ text-align: right;
+}
+footer p {
+ margin-bottom: 0;
+}
+
+img.icon {
+ float: right;
+}
+
+img {
+ max-width: 100%;
+}
+
+/* Section anchors ---------------------------------*/
+
+a.anchor {
+ margin-left: -30px;
+ display:inline-block;
+ width: 30px;
+ height: 30px;
+ visibility: hidden;
+
+ background-image: url(./link.svg);
+ background-repeat: no-repeat;
+ background-size: 20px 20px;
+ background-position: center center;
+}
+
+.hasAnchor:hover a.anchor {
+ visibility: visible;
+}
+
+@media (max-width: 767px) {
+ .hasAnchor:hover a.anchor {
+ visibility: hidden;
+ }
+}
+
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+ padding-top: 60px;
+ margin-top: -60px;
+}
+
+/* Static header placement on mobile devices */
+@media (max-width: 767px) {
+ .navbar-fixed-top {
+ position: absolute;
+ }
+ .navbar {
+ padding: 0;
+ }
+}
+
+
+/* Sidebar --------------------------*/
+
+#sidebar {
+ margin-top: 30px;
+}
+#sidebar h2 {
+ font-size: 1.5em;
+ margin-top: 1em;
+}
+
+#sidebar h2:first-child {
+ margin-top: 0;
+}
+
+#sidebar .list-unstyled li {
+ margin-bottom: 0.5em;
+}
+
+/* Reference index & topics ----------------------------------------------- */
+
+.ref-index th {font-weight: normal;}
+.ref-index h2 {font-size: 20px;}
+
+.ref-index td {vertical-align: top;}
+.ref-index .alias {width: 40%;}
+.ref-index .title {width: 60%;}
+
+.ref-index .alias {width: 40%;}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top;}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+ display: block;
+ overflow: auto;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+pre {
+ word-wrap: normal;
+ word-break: normal;
+ border: 1px solid #eee;
+}
+
+pre, code {
+ background-color: #f8f8f8;
+ color: #333;
+}
+
+pre .img {
+ margin: 5px 0;
+}
+
+pre .img img {
+ background-color: #fff;
+ display: block;
+ height: auto;
+}
+
+code a, pre a {
+ color: #375f84;
+}
+
+.fl {color: #1514b5;}
+.fu {color: #000000;} /* function */
+.ch,.st {color: #036a07;} /* string */
+.kw {color: #264D66;} /* keyword */
+.co {color: #888888;} /* comment */
+
+.message { color: black; font-weight: bolder;}
+.error { color: orange; font-weight: bolder;}
+.warning { color: #6A0366; font-weight: bolder;}
+
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
new file mode 100644
index 0000000000000000000000000000000000000000..4b81713289040dbd19cf8e215a054f5c129a5f91
--- /dev/null
+++ b/docs/pkgdown.js
@@ -0,0 +1,45 @@
+$(function() {
+ $("#sidebar").stick_in_parent({offset_top: 40});
+ $('body').scrollspy({
+ target: '#sidebar',
+ offset: 60
+ });
+
+ var cur_path = paths(location.pathname);
+ $("#navbar ul li a").each(function(index, value) {
+ if (value.text == "Home")
+ return;
+ if (value.getAttribute("href") === "#")
+ return;
+
+ var path = paths(value.pathname);
+ if (is_prefix(cur_path, path)) {
+ // Add class to parent <li>, and enclosing <li> if in dropdown
+ var menu_anchor = $(value);
+ menu_anchor.parent().addClass("active");
+ menu_anchor.closest("li.dropdown").addClass("active");
+ }
+ });
+});
+
+function paths(pathname) {
+ var pieces = pathname.split("/");
+ pieces.shift(); // always starts with /
+
+ var end = pieces[pieces.length - 1];
+ if (end === "index.html" || end === "")
+ pieces.pop();
+ return(pieces);
+}
+
+function is_prefix(needle, haystack) {
+ if (needle.length > haystack.lengh)
+ return(false);
+
+ for (var i = 0; i < haystack.length; i++) {
+ if (needle[i] != haystack[i])
+ return(false);
+ }
+
+ return(true);
+}
diff --git a/docs/reference/Lun2Params.html b/docs/reference/Lun2Params.html
new file mode 100644
index 0000000000000000000000000000000000000000..9778ab17d2951eb86b0077b7a253e24b51a5245c
--- /dev/null
+++ b/docs/reference/Lun2Params.html
@@ -0,0 +1,164 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>The Lun2Params class — Lun2Params • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The Lun2Params class</h1>
+ </div>
+
+
+ <p>S4 class that holds parameters for the Lun simulation.</p>
+
+
+
+ <h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
+
+
+ <p>The Lun2 simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
+ <dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
+ <dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+ <dt><em>Gene parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>gene.params</code></dt><dd><p>A <code>data.frame</code> containing gene
+ parameters with two coloumns: <code>Mean</code> (mean expression for
+ each gene) and <code>Disp</code> (dispersion for each gene).</p></dd>
+ <dt><code>zi.params</code></dt><dd><p>A <code>data.frame</code> containing
+ zero-inflated gene parameters with three coloumns: <code>Mean</code>
+ (mean expression for each gene), <code>Disp</code> (dispersion for
+ each, gene), and <code>Prop</code> (zero proportion for each gene).</p></dd>
+ </dl></p></dd>
+ <dt><code>[nPlates]</code></dt><dd><p>The number of plates to simulate.</p></dd>
+ <dt><em>Plate parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>plate.ingroup</code></dt><dd><p>Character vecotor giving the plates
+ considered to be part of the "ingroup".</p></dd>
+ <dt><code>plate.mod</code></dt><dd><p>Plate effect modifier factor. The plate
+ effect variance is divided by this value.</p></dd>
+ <dt><code>plate.var</code></dt><dd><p>Plate effect variance.</p></dd>
+ </dl></p></dd>
+ <dt><em>Cell parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>cell.plates</code></dt><dd><p>Factor giving the plate that each cell
+ comes from.</p></dd>
+ <dt><code>cell.libSizes</code></dt><dd><p>Library size for each cell.</p></dd>
+ <dt><code>cell.libMod</code></dt><dd><p>Modifier factor for library sizes.
+ The library sizes are multiplied by this value.</p></dd>
+ </dl></p></dd>
+ <dt><em>Differential expression parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>de.nGenes</code></dt><dd><p>Number of differentially expressed
+ genes.</p></dd>
+ <dt><code>de.fc</code></dt><dd><p>Fold change for differentially expressed
+ genes.</p></dd>
+ </dl></p></dd>
+</dl>
+ <p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='lun2Estimate.html'>lun2Estimate</a></code>. For details of the Lun2 simulation see
+<code><a href='lun2Simulate.html'>lun2Simulate</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/LunParams.html b/docs/reference/LunParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..aeb89fc0f739258f55149ec5c83add3bd22bf6fc
--- /dev/null
+++ b/docs/reference/LunParams.html
@@ -0,0 +1,156 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>The LunParams class — LunParams • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The LunParams class</h1>
+ </div>
+
+
+ <p>S4 class that holds parameters for the Lun simulation.</p>
+
+
+
+ <h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
+
+
+ <p>The Lun simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
+ <dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
+ <dt><code>[nGroups]</code></dt><dd><p>The number of groups to simulate.</p></dd>
+ <dt><code>[groupCells]</code></dt><dd><p>Vector giving the number of cells in each
+ simulation group/path.</p></dd>
+ <dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+ <dt><em>Mean parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[mean.shape]</code></dt><dd><p>Shape parameter for the mean gamma
+ distribution.</p></dd>
+ <dt><code>[mean.rate]</code></dt><dd><p>Rate parameter for the mean gamma
+ distribution.</p></dd>
+ </dl></p></dd>
+ <dt><em>Counts parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[count.disp]</code></dt><dd><p>The dispersion parameter for the
+ counts negative binomial distribution.</p></dd>
+ </dl></p></dd>
+ <dt><em>Differential expression parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[de.nGenes]</code></dt><dd><p>The number of genes that are
+ differentially expressed in each group</p></dd>
+ <dt><code>[de.upProp]</code></dt><dd><p>The proportion of differentially
+ expressed genes that are up-regulated in each group</p></dd>
+ <dt><code>[de.upFC]</code></dt><dd><p>The fold change for up-regulated genes</p></dd>
+ <dt><code>[de.downFC]</code></dt><dd><p>The fold change for down-regulated
+ genes</p></dd>
+ </dl></p></dd>
+</dl>
+ <p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='lunEstimate.html'>lunEstimate</a></code>. For details of the Lun simulation see
+<code><a href='lunSimulate.html'>lunSimulate</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/Params.html b/docs/reference/Params.html
new file mode 100644
index 0000000000000000000000000000000000000000..4106d3765c92fb2d9c6f6a11c1435039fd8d11f4
--- /dev/null
+++ b/docs/reference/Params.html
@@ -0,0 +1,132 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>The Params virtual class — Params • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The Params virtual class</h1>
+ </div>
+
+
+ <p>Virtual S4 class that all other Params classes inherit from.</p>
+
+
+
+ <h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
+
+
+ <p>The Params class defines the following parameters:</p><dl class='dl-horizontal'>
+ <dt><code>[nGenes]</code></dt><dd><p>The number of genes to simulate.</p></dd>
+ <dt><code>[nCells]</code></dt><dd><p>The number of cells to simulate.</p></dd>
+ <dt><code>seed</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+</dl>
+ <p>The parameters shown in brackets can be estimated from real data.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/SCDDParams.html b/docs/reference/SCDDParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..5fcca8c99121430b4419b32d9ee319a6d649a91e
--- /dev/null
+++ b/docs/reference/SCDDParams.html
@@ -0,0 +1,149 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>The SCDDParams class — SCDDParams • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The SCDDParams class</h1>
+ </div>
+
+
+ <p>S4 class that holds parameters for the scDD simulation.</p>
+
+
+
+ <h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
+
+
+ <p>The SCDD simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <dt><code>nGenes</code></dt><dd><p>The number of genes to simulate (not used).</p></dd>
+ <dt><code>nCells</code></dt><dd><p>The number of cells to simulate in each condition.</p></dd>
+ <dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+ <dt><code>SCdat</code></dt><dd><p><code><a href='http://www.rdocumentation.org/packages/SummarizedExperiment/topics/RangedSummarizedExperiment-class'>SummarizedExperiment</a></code> containing real
+ data.</p></dd>
+ <dt><code>nDE</code></dt><dd><p>Number of DE genes to simulate.</p></dd>
+ <dt><code>nDP</code></dt><dd><p>Number of DP genes to simulate.</p></dd>
+ <dt><code>nDM</code></dt><dd><p>Number of DM genes to simulate.</p></dd>
+ <dt><code>nDB</code></dt><dd><p>Number of DB genes to simulate.</p></dd>
+ <dt><code>nEE</code></dt><dd><p>Number of EE genes to simulate.</p></dd>
+ <dt><code>nEP</code></dt><dd><p>Number of EP genes to simulate.</p></dd>
+ <dt><code>[sd.range]</code></dt><dd><p>Interval for fold change standard deviations.</p></dd>
+ <dt><code>[modeFC]</code></dt><dd><p>Values for DP, DM and DB mode fold changes.</p></dd>
+ <dt><code>[varInflation]</code></dt><dd><p>Variance inflation factors for each
+ condition. If all equal to 1 will be set to <code>NULL</code> (default).</p></dd>
+ <dt><code>[condition]</code></dt><dd><p>String giving the column that represents
+ biological group of interest.</p></dd>
+</dl>
+ <p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='scDDEstimate.html'>scDDEstimate</a></code>. See <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> for more
+details of the parameters. For details of the Splatter implementation of the
+scDD simulation see <code><a href='scDDSimulate.html'>scDDSimulate</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/SimpleParams.html b/docs/reference/SimpleParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..199f0ea31bccbb2b85f3b148a27917296af1018c
--- /dev/null
+++ b/docs/reference/SimpleParams.html
@@ -0,0 +1,140 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>The SimpleParams class — SimpleParams • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The SimpleParams class</h1>
+ </div>
+
+
+ <p>S4 class that holds parameters for the simple simulation.</p>
+
+
+
+ <h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
+
+
+ <p>The simple simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
+ <dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
+ <dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+ <dt><code>mean.shape</code></dt><dd><p>The shape parameter for the mean gamma
+ distribution.</p></dd>
+ <dt><code>mean.rate</code></dt><dd><p>The rate parameter for the mean gamma
+ distribution.</p></dd>
+ <dt><code>[count.disp]</code></dt><dd><p>The dispersion parameter for the counts
+ negative binomial distribution.</p></dd>
+</dl>
+ <p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='simpleEstimate.html'>simpleEstimate</a></code>. For details of the simple simulation
+see <code><a href='simpleSimulate.html'>simpleSimulate</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/SplatParams.html b/docs/reference/SplatParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..a0514095f3e8cd58c3e1a9cc1faca881dda477a3
--- /dev/null
+++ b/docs/reference/SplatParams.html
@@ -0,0 +1,220 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>The SplatParams class — SplatParams • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The SplatParams class</h1>
+ </div>
+
+
+ <p>S4 class that holds parameters for the Splatter simulation.</p>
+
+
+
+ <h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
+
+
+ <p>The Splatter simulation requires the following parameters:</p><dl class='dl-horizontal'>
+ <dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
+ <dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
+ <dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+ <dt><em>Batch parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[nBatches]</code></dt><dd><p>The number of batches to simulate.</p></dd>
+ <dt><code>[batchCells]</code></dt><dd><p>Vector giving the number of cells in
+ each batch.</p></dd>
+ <dt><code>[batch.facLoc]</code></dt><dd><p>Location (meanlog) parameter for the
+ batch effect factor log-normal distribution. Can be a vector.</p></dd>
+ <dt><code>[batch.facScale]</code></dt><dd><p>Scale (sdlog) parameter for the
+ batch effect factor log-normal distribution. Can be a vector.</p></dd>
+ </dl></p></dd>
+ <dt><em>Mean parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>mean.shape</code></dt><dd><p>Shape parameter for the mean gamma
+ distribution.</p></dd>
+ <dt><code>mean.rate</code></dt><dd><p>Rate parameter for the mean gamma
+ distribution.</p></dd>
+ </dl></p></dd>
+ <dt><em>Library size parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>lib.loc</code></dt><dd><p>Location (meanlog) parameter for the
+ library size log-normal distribution.</p></dd>
+ <dt><code>lib.scale</code></dt><dd><p>Scale (sdlog) parameter for the library
+ size log-normal distribution.</p></dd>
+ </dl></p></dd>
+ <dt><em>Expression outlier parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>out.prob</code></dt><dd><p>Probability that a gene is an expression
+ outlier.</p></dd>
+ <dt><code>out.facLoc</code></dt><dd><p>Location (meanlog) parameter for the
+ expression outlier factor log-normal distribution.</p></dd>
+ <dt><code>out.facScale</code></dt><dd><p>Scale (sdlog) parameter for the
+ expression outlier factor log-normal distribution.</p></dd>
+ </dl></p></dd>
+ <dt><em>Group parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[nGroups]</code></dt><dd><p>The number of groups or paths to
+ simulate.</p></dd>
+ <dt><code>[group.prob]</code></dt><dd><p>Probability that a cell comes from a
+ group.</p></dd>
+ </dl></p></dd>
+ <dt><em>Differential expression parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[de.prob]</code></dt><dd><p>Probability that a gene is differentially
+ expressed in a group. Can be a vector.</p></dd>
+ <dt><code>[de.loProb]</code></dt><dd><p>Probability that a differentially
+ expressed gene is down-regulated. Can be a vector.</p></dd>
+ <dt><code>[de.facLoc]</code></dt><dd><p>Location (meanlog) parameter for the
+ differential expression factor log-normal distribution. Can be a
+ vector.</p></dd>
+ <dt><code>[de.facScale]</code></dt><dd><p>Scale (sdlog) parameter for the
+ differential expression factor log-normal distribution. Can be a
+ vector.</p></dd>
+ </dl></p></dd>
+ <dt><em>Biological Coefficient of Variation parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>bcv.common</code></dt><dd><p>Underlying common dispersion across all
+ genes.</p></dd>
+ <dt><code>bcv.df</code></dt><dd><p>Degrees of Freedom for the BCV inverse
+ chi-squared distribution.</p></dd>
+ </dl></p></dd>
+ <dt><em>Dropout parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>dropout.present</code></dt><dd><p>Logical. Whether to simulate
+ dropout.</p></dd>
+ <dt><code>dropout.mid</code></dt><dd><p>Midpoint parameter for the dropout
+ logistic function.</p></dd>
+ <dt><code>dropout.shape</code></dt><dd><p>Shape parameter for the dropout
+ logistic function.</p></dd>
+ </dl></p></dd>
+ <dt><em>Differentiation path parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[path.from]</code></dt><dd><p>Vector giving the originating point of
+ each path. This allows path structure such as a cell type which
+ differentiates into an intermediate cell type that then
+ differentiates into two mature cell types. A path structure of
+ this form would have a "from" parameter of c(0, 1, 1) (where 0 is
+ the origin). If no vector is given all paths will start at the
+ origin.</p></dd>
+ <dt><code>[path.length]</code></dt><dd><p>Vector giving the number of steps to
+ simulate along each path. If a single value is given it will be
+ applied to all paths.</p></dd>
+ <dt><code>[path.skew]</code></dt><dd><p>Vector giving the skew of each path.
+ Values closer to 1 will give more cells towards the starting
+ population, values closer to 0 will give more cells towards the
+ final population. If a single value is given it will be applied
+ to all paths.</p></dd>
+ <dt><code>[path.nonlinearProb]</code></dt><dd><p>Probability that a gene
+ follows a non-linear path along the differentiation path. This
+ allows more complex gene patterns such as a gene being equally
+ expressed at the beginning an end of a path but lowly expressed
+ in the middle.</p></dd>
+ <dt><code>[path.sigmaFac]</code></dt><dd><p>Sigma factor for non-linear gene
+ paths. A higher value will result in more extreme non-linear
+ variations along a path.</p></dd>
+ </dl></p></dd>
+</dl>
+ <p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='splatEstimate.html'>splatEstimate</a></code>. For details of the Splatter simulation
+see <code><a href='splatSimulate.html'>splatSimulate</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/addFeatureStats.html b/docs/reference/addFeatureStats.html
new file mode 100644
index 0000000000000000000000000000000000000000..494cfa8a510c1994e717394eaa2fa8753320e626
--- /dev/null
+++ b/docs/reference/addFeatureStats.html
@@ -0,0 +1,168 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Add feature statistics — addFeatureStats • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Add feature statistics</h1>
+ </div>
+
+
+ <p>Add additional feature statistics to an SCESet object</p>
+
+
+ <pre class="usage"><span class='fu'>addFeatureStats</span>(<span class='no'>sce</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"counts"</span>, <span class='st'>"cpm"</span>, <span class='st'>"tpm"</span>, <span class='st'>"fpkm"</span>), <span class='kw'>log</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>offset</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>no.zeros</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sce</th>
+ <td><p>SCESet to add feature statistics to.</p></td>
+ </tr>
+ <tr>
+ <th>value</th>
+ <td><p>the expression value to calculate statistics for. Options are
+"counts", "cpm", "tpm" or "fpkm". The values need to exist in the
+given SCESet.</p></td>
+ </tr>
+ <tr>
+ <th>log</th>
+ <td><p>logical. Whether to take log2 before calculating statistics.</p></td>
+ </tr>
+ <tr>
+ <th>offset</th>
+ <td><p>offset to add to avoid taking log of zero.</p></td>
+ </tr>
+ <tr>
+ <th>no.zeros</th>
+ <td><p>logical. Whether to remove all zeros from each feature before
+calculating statistics.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with additional feature statistics</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Currently adds the following statistics: mean, variance, coefficient of
+variation, median and median absolute deviation. Statistics are added to
+the <code>fData</code> slot and are named <code>Stat[Log]Value[No0]</code> where
+<code>Log</code> and <code>No0</code> are added if those arguments are true.
+UpperCamelCase is used to differentiate these columns from those added by
+<code>scater</code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
new file mode 100644
index 0000000000000000000000000000000000000000..9de96077c2c7048a13c979fa1162682d5c17f489
--- /dev/null
+++ b/docs/reference/addGeneLengths.html
@@ -0,0 +1,187 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Add gene lengths — addGeneLengths • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Add gene lengths</h1>
+ </div>
+
+
+ <p>Add gene lengths to an SCESet object</p>
+
+
+ <pre class="usage"><span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"generate"</span>, <span class='st'>"sample"</span>), <span class='kw'>loc</span> <span class='kw'>=</span> <span class='fl'>7.9</span>,
+ <span class='kw'>scale</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>lengths</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sce</th>
+ <td><p>SCESet to add gene lengths to.</p></td>
+ </tr>
+ <tr>
+ <th>method</th>
+ <td><p>Method to use for creating lengths.</p></td>
+ </tr>
+ <tr>
+ <th>loc</th>
+ <td><p>Location parameter for the generate method.</p></td>
+ </tr>
+ <tr>
+ <th>scale</th>
+ <td><p>Scale parameter for the generate method.</p></td>
+ </tr>
+ <tr>
+ <th>lengths</th>
+ <td><p>Vector of lengths for the sample method.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with added gene lengths</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function adds simulated gene lengths to the <code>fData</code> slot of an
+<code>SCESet</code> object that can be used for calculating length normalised
+expression values such as TPM or FPKM. The <code>generate</code> simulates lengths
+using a (rounded) log-normal distribution, with the default <code>loc</code> and
+<code>scale</code> parameters based on human coding genes. Alternatively the
+<code>sample</code> method can be used which randomly samples lengths (with
+replacement) from a supplied vector.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># Default generate method</span>
+<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
+<span class='fu'>head</span>(<span class='fu'>fData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> Gene GeneMean Length
+#> Gene1 Gene1 0.38438825 1985
+#> Gene2 Gene2 0.24016850 1279
+#> Gene3 Gene3 2.79407135 3625
+#> Gene4 Gene4 0.07108685 1992
+#> Gene5 Gene5 0.56586620 7394
+#> Gene6 Gene6 0.01464522 1704</div><div class='input'># Sample method (human coding genes)
+</div><span class='co'># NOT RUN {</span>
+<span class='fu'>library</span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
+<span class='fu'>library</span>(<span class='no'>GenomicFeatures</span>)
+<span class='no'>txdb</span> <span class='kw'><-</span> <span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>
+<span class='no'>tx.lens</span> <span class='kw'><-</span> <span class='fu'>transcriptLengths</span>(<span class='no'>txdb</span>, <span class='kw'>with.cds_len</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>tx.lens</span> <span class='kw'><-</span> <span class='no'>tx.lens</span>[<span class='no'>tx.lens</span>$<span class='no'>cds_len</span> <span class='kw'>></span> <span class='fl'>0</span>, ]
+<span class='no'>gene.lens</span> <span class='kw'><-</span> <span class='fu'>max</span>(<span class='fu'>splitAsList</span>(<span class='no'>tx.lens</span>$<span class='no'>tx_len</span>, <span class='no'>tx.lens</span>$<span class='no'>gene_id</span>))
+<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"sample"</span>, <span class='kw'>lengths</span> <span class='kw'>=</span> <span class='no'>gene.lens</span>)
+<span class='co'># }</span></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/bridge.html b/docs/reference/bridge.html
new file mode 100644
index 0000000000000000000000000000000000000000..014948a4f84b6d2024ee15444987cc199981d973
--- /dev/null
+++ b/docs/reference/bridge.html
@@ -0,0 +1,154 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Brownian bridge — bridge • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Brownian bridge</h1>
+ </div>
+
+
+ <p>Calculate a smoothed Brownian bridge between two points. A Brownian bridge is
+a random walk with fixed end points.</p>
+
+
+ <pre class="usage"><span class='fu'>bridge</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>sigma.fac</span> <span class='kw'>=</span> <span class='fl'>0.8</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>starting value.</p></td>
+ </tr>
+ <tr>
+ <th>y</th>
+ <td><p>end value.</p></td>
+ </tr>
+ <tr>
+ <th>N</th>
+ <td><p>number of steps in random walk.</p></td>
+ </tr>
+ <tr>
+ <th>n</th>
+ <td><p>number of points in smoothed bridge.</p></td>
+ </tr>
+ <tr>
+ <th>sigma.fac</th>
+ <td><p>multiplier specifying how extreme each step can be.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Vector of length n following a path from x to y.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/compareSCESets.html b/docs/reference/compareSCESets.html
new file mode 100644
index 0000000000000000000000000000000000000000..dc2806ad0bc3109bdecb98fda9d031e5ff5ca28f
--- /dev/null
+++ b/docs/reference/compareSCESets.html
@@ -0,0 +1,191 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Compare SCESet objects — compareSCESets • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Compare SCESet objects</h1>
+ </div>
+
+
+ <p>Combine the data from several SCESet objects and produce some basic plots
+comparing them.</p>
+
+
+ <pre class="usage"><span class='fu'>compareSCESets</span>(<span class='no'>sces</span>, <span class='kw'>point.size</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>fits</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>colours</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sces</th>
+ <td><p>named list of SCESet objects to combine and compare.</p></td>
+ </tr>
+ <tr>
+ <th>point.size</th>
+ <td><p>size of points in scatter plots.</p></td>
+ </tr>
+ <tr>
+ <th>point.alpha</th>
+ <td><p>opacity of points in scatter plots.</p></td>
+ </tr>
+ <tr>
+ <th>fits</th>
+ <td><p>whether to include fits in scatter plots.</p></td>
+ </tr>
+ <tr>
+ <th>colours</th>
+ <td><p>vector of colours to use for each dataset.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>List containing the combined datasets and plots.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The returned list has three items:</p><dl class='dl-horizontal'>
+ <dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
+ SCESets.</p></dd>
+ <dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided SCESets.</p></dd>
+ <dt><code>Plots</code></dt><dd><p>Comparison plots
+ <dl class='dl-horizontal'>
+ <dt><code>Means</code></dt><dd><p>Boxplot of mean distribution.</p></dd>
+ <dt><code>Variances</code></dt><dd><p>Boxplot of variance distribution.</p></dd>
+ <dt><code>MeanVar</code></dt><dd><p>Scatter plot with fitted lines showing the
+ mean-variance relationship.</p></dd>
+ <dt><code>LibraySizes</code></dt><dd><p>Boxplot of the library size
+ distribution.</p></dd>
+ <dt><code>ZerosGene</code></dt><dd><p>Boxplot of the percentage of each gene
+ that is zero.</p></dd>
+ <dt><code>ZerosCell</code></dt><dd><p>Boxplot of the percentage of each cell
+ that is zero.</p></dd>
+ <dt><code>MeanZeros</code></dt><dd><p>Scatter plot with fitted lines showing
+ the mean-zeros relationship.</p></dd>
+ </dl></p></dd>
+</dl>
+ <p>The plots returned by this function are created using
+<code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
+might like to consider. The data used to create these plots is also returned
+and should be in the correct format to allow you to create further plots
+using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts..</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCESets</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#> [1] "FeatureData" "PhenoData" "Plots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
+#> [6] "ZerosCell" "MeanZeros" </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/diffSCESets.html b/docs/reference/diffSCESets.html
new file mode 100644
index 0000000000000000000000000000000000000000..fd74d5c9932e4ed116ec7e6072ad5c23fdf58f01
--- /dev/null
+++ b/docs/reference/diffSCESets.html
@@ -0,0 +1,211 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Diff SCESet objects — diffSCESets • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Diff SCESet objects</h1>
+ </div>
+
+
+ <p>Combine the data from several SCESet objects and produce some basic plots
+comparing them to a reference.</p>
+
+
+ <pre class="usage"><span class='fu'>diffSCESets</span>(<span class='no'>sces</span>, <span class='no'>ref</span>, <span class='kw'>point.size</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>fits</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>colours</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sces</th>
+ <td><p>named list of SCESet objects to combine and compare.</p></td>
+ </tr>
+ <tr>
+ <th>ref</th>
+ <td><p>string giving the name of the SCESet to use as the reference</p></td>
+ </tr>
+ <tr>
+ <th>point.size</th>
+ <td><p>size of points in scatter plots.</p></td>
+ </tr>
+ <tr>
+ <th>point.alpha</th>
+ <td><p>opacity of points in scatter plots.</p></td>
+ </tr>
+ <tr>
+ <th>fits</th>
+ <td><p>whether to include fits in scatter plots.</p></td>
+ </tr>
+ <tr>
+ <th>colours</th>
+ <td><p>vector of colours to use for each dataset.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>List containing the combined datasets and plots.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function aims to look at the differences between a reference SCESet and
+one or more others. It requires each SCESet to have the same dimensions.
+Properties are compared by ranks, for example when comparing the means the
+values are ordered and the differences between the reference and another
+dataset plotted. A series of Q-Q plots are also returned.</p>
+<p>The returned list has five items:</p><dl class='dl-horizontal'>
+ <dt><code>Reference</code></dt><dd><p>The SCESet used as the reference.</p></dd>
+ <dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
+ SCESets.</p></dd>
+ <dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided SCESets.</p></dd>
+ <dt><code>Plots</code></dt><dd><p>Difference plots
+ <dl class='dl-horizontal'>
+ <dt><code>Means</code></dt><dd><p>Boxplot of mean differences.</p></dd>
+ <dt><code>Variances</code></dt><dd><p>Boxplot of variance differences.</p></dd>
+ <dt><code>MeanVar</code></dt><dd><p>Scatter plot showing the difference from
+ the reference variance across expression ranks.</p></dd>
+ <dt><code>LibraySizes</code></dt><dd><p>Boxplot of the library size
+ differences.</p></dd>
+ <dt><code>ZerosGene</code></dt><dd><p>Boxplot of the differences in the
+ percentage of each gene that is zero.</p></dd>
+ <dt><code>ZerosCell</code></dt><dd><p>Boxplot of the differences in the
+ percentage of each cell that is zero.</p></dd>
+ <dt><code>MeanZeros</code></dt><dd><p>Scatter plot showing the difference from
+ the reference percentage of zeros across expression ranks.</p></dd>
+ </dl></p></dd>
+ <dt><code>QQPlots</code></dt><dd><p>Quantile-Quantile plots
+ <dl class='dl-horizontal'>
+ <dt><code>Means</code></dt><dd><p>Q-Q plot of the means.</p></dd>
+ <dt><code>Variances</code></dt><dd><p>Q-Q plot of the variances.</p></dd>
+ <dt><code>LibrarySizes</code></dt><dd><p>Q-Q plot of the library sizes.</p></dd>
+ <dt><code>ZerosGene</code></dt><dd><p>Q-Q plot of the percentage of zeros per
+ gene.</p></dd>
+ <dt><code>ZerosCell</code></dt><dd><p>Q-Q plot of the percentage of zeros per
+ cell.</p></dd>
+ </dl></p></dd>
+</dl>
+ <p>The plots returned by this function are created using
+<code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
+might like to consider. The data used to create these plots is also returned
+and should be in the correct format to allow you to create further plots
+using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts..</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCESets</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#> [1] "Reference" "FeatureData" "PhenoData" "Plots" "QQPlots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
+#> [6] "ZerosCell" "MeanZeros" </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/expandParams.html b/docs/reference/expandParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..a94a2354a278db5d365d84a47e89e61ebbcd6e69
--- /dev/null
+++ b/docs/reference/expandParams.html
@@ -0,0 +1,148 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Expand parameters — expandParams • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Expand parameters</h1>
+ </div>
+
+
+ <p>Expand the parameters that can be vectors so that they are the same length as
+the number of groups.</p>
+
+
+ <pre class="usage"><span class='fu'>expandParams</span>(<span class='no'>object</span>, <span class='no'>...</span>)
+
+<span class='co'># S4 method for LunParams</span>
+<span class='fu'>expandParams</span>(<span class='no'>object</span>)
+
+<span class='co'># S4 method for SplatParams</span>
+<span class='fu'>expandParams</span>(<span class='no'>object</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>object to expand.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>additional arguments.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Expanded object.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/getLNormFactors.html b/docs/reference/getLNormFactors.html
new file mode 100644
index 0000000000000000000000000000000000000000..f792b2ff2f1d6e7ef6c0fa3100ae3dd2a3b5f7fd
--- /dev/null
+++ b/docs/reference/getLNormFactors.html
@@ -0,0 +1,154 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Get log-normal factors — getLNormFactors • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Get log-normal factors</h1>
+ </div>
+
+
+ <p>Randomly generate multiplication factors from a log-normal distribution.</p>
+
+
+ <pre class="usage"><span class='fu'>getLNormFactors</span>(<span class='no'>n.facs</span>, <span class='no'>sel.prob</span>, <span class='no'>neg.prob</span>, <span class='no'>fac.loc</span>, <span class='no'>fac.scale</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>n.facs</th>
+ <td><p>Number of factors to generate.</p></td>
+ </tr>
+ <tr>
+ <th>sel.prob</th>
+ <td><p>Probability that a factor will be selected to be different
+from 1.</p></td>
+ </tr>
+ <tr>
+ <th>neg.prob</th>
+ <td><p>Probability that a selected factor is less than one.</p></td>
+ </tr>
+ <tr>
+ <th>fac.loc</th>
+ <td><p>Location parameter for the log-normal distribution.</p></td>
+ </tr>
+ <tr>
+ <th>fac.scale</th>
+ <td><p>Scale factor for the log-normal distribution.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Vector containing generated factors.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html
new file mode 100644
index 0000000000000000000000000000000000000000..65e5438b498d58b1d91a73411de58df95b44b723
--- /dev/null
+++ b/docs/reference/getParam.html
@@ -0,0 +1,150 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Get a parameter — getParam • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Get a parameter</h1>
+ </div>
+
+
+ <p>Accessor function for getting parameter values.</p>
+
+
+ <pre class="usage"><span class='fu'>getParam</span>(<span class='no'>object</span>, <span class='no'>name</span>)
+
+<span class='co'># S4 method for Params</span>
+<span class='fu'>getParam</span>(<span class='no'>object</span>, <span class='no'>name</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>object to get parameter from.</p></td>
+ </tr>
+ <tr>
+ <th>name</th>
+ <td><p>name of the parameter to get.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The extracted parameter value</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
+<span class='fu'>getParam</span>(<span class='no'>params</span>, <span class='st'>"nGenes"</span>)</div><div class='output co'>#> [1] 10000</div><div class='input'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/getParams.html b/docs/reference/getParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..36d1e9091274ba89bbdde6dc34b09868d0ee8609
--- /dev/null
+++ b/docs/reference/getParams.html
@@ -0,0 +1,154 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Get parameters — getParams • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Get parameters</h1>
+ </div>
+
+
+ <p>Get multiple parameter values from a Params object.</p>
+
+
+ <pre class="usage"><span class='fu'>getParams</span>(<span class='no'>params</span>, <span class='no'>names</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>Params object to get values from.</p></td>
+ </tr>
+ <tr>
+ <th>names</th>
+ <td><p>vector of names of the parameters to get.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>List with the values of the selected parameters.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
+<span class='fu'>getParams</span>(<span class='no'>params</span>, <span class='fu'>c</span>(<span class='st'>"nGenes"</span>, <span class='st'>"nCells"</span>, <span class='st'>"mean.rate"</span>))</div><div class='output co'>#> $nGenes
+#> [1] 10000
+#>
+#> $nCells
+#> [1] 100
+#>
+#> $mean.rate
+#> [1] 0.3
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/getPathOrder.html b/docs/reference/getPathOrder.html
new file mode 100644
index 0000000000000000000000000000000000000000..2e80be192cd571a5e1bd6d0702bf4814e876e68c
--- /dev/null
+++ b/docs/reference/getPathOrder.html
@@ -0,0 +1,139 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Get path order — getPathOrder • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Get path order</h1>
+ </div>
+
+
+ <p>Identify the correct order to process paths so that preceding paths have
+already been simulated.</p>
+
+
+ <pre class="usage"><span class='fu'>getPathOrder</span>(<span class='no'>path.from</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>path.from</th>
+ <td><p>vector giving the path endpoints that each path orginates
+from.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Vector giving the order to process paths in.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/index.html b/docs/reference/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..218ccd018534fa8bf78d9df9ca257aa12c491188
--- /dev/null
+++ b/docs/reference/index.html
@@ -0,0 +1,467 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Function reference • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-index">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9">
+ <div class="page-header">
+ <h1>
+ Reference
+ <small>version 1.1.4</small>
+ </h1>
+ </div>
+
+ <div class="contents">
+ <table class="ref-index">
+
+ <colgroup>
+ <col class="alias" />
+ <col class="title" />
+ </colgroup>
+
+ <tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
+ <p class="section-desc"></p>
+ </th>
+ </tr>
+ <tr>
+ <!-- -->
+ <td>
+ <p><code><a href="addFeatureStats.html">addFeatureStats</a></code> </p>
+ </td>
+ <td><p>Add feature statistics</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="addGeneLengths.html">addGeneLengths</a></code> </p>
+ </td>
+ <td><p>Add gene lengths</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="bridge.html">bridge</a></code> </p>
+ </td>
+ <td><p>Brownian bridge</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="compareSCESets.html">compareSCESets</a></code> </p>
+ </td>
+ <td><p>Compare SCESet objects</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="diffSCESets.html">diffSCESets</a></code> </p>
+ </td>
+ <td><p>Diff SCESet objects</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="expandParams.html">expandParams</a></code> </p>
+ </td>
+ <td><p>Expand parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="getLNormFactors.html">getLNormFactors</a></code> </p>
+ </td>
+ <td><p>Get log-normal factors</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="getParam.html">getParam</a></code> </p>
+ </td>
+ <td><p>Get a parameter</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="getParams.html">getParams</a></code> </p>
+ </td>
+ <td><p>Get parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="getPathOrder.html">getPathOrder</a></code> </p>
+ </td>
+ <td><p>Get path order</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="listSims.html">listSims</a></code> </p>
+ </td>
+ <td><p>List simulations</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="logistic.html">logistic</a></code> </p>
+ </td>
+ <td><p>Logistic function</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="lun2Estimate.html">lun2Estimate</a></code> </p>
+ </td>
+ <td><p>Estimate Lun2 simulation parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>The Lun2Params class</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="lun2Simulate.html">lun2Simulate</a></code> </p>
+ </td>
+ <td><p>Lun2 simulation</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="lunEstimate.html">lunEstimate</a></code> </p>
+ </td>
+ <td><p>Estimate Lun simulation parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>The LunParams class</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="lunSimulate.html">lunSimulate</a></code> </p>
+ </td>
+ <td><p>Lun simulation</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="makeCompPanel.html">makeCompPanel</a></code> </p>
+ </td>
+ <td><p>Make comparison panel</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="makeDiffPanel.html">makeDiffPanel</a></code> </p>
+ </td>
+ <td><p>Make difference panel</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="makeOverallPanel.html">makeOverallPanel</a></code> </p>
+ </td>
+ <td><p>Make overall panel</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="newParams.html">newLun2Params</a></code> <code><a href="newParams.html">newLunParams</a></code> <code><a href="newParams.html">newSCDDParams</a></code> <code><a href="newParams.html">newSimpleParams</a></code> <code><a href="newParams.html">newSplatParams</a></code> </p>
+ </td>
+ <td><p>New Params</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>The Params virtual class</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="rbindMatched.html">rbindMatched</a></code> </p>
+ </td>
+ <td><p>Bind rows (matched)</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="scDDEstimate.html">scDDEstimate</a></code> </p>
+ </td>
+ <td><p>Estimate scDD simulation parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>The SCDDParams class</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="scDDSimulate.html">scDDSimulate</a></code> </p>
+ </td>
+ <td><p>scDD simulation</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="setParam.html">setParam</a></code> </p>
+ </td>
+ <td><p>Set a parameter</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="setParams.html">setParams</a></code> </p>
+ </td>
+ <td><p>Set parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="setParamsUnchecked.html">setParamsUnchecked</a></code> </p>
+ </td>
+ <td><p>Set parameters UNCHECKED</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="setParamUnchecked.html">setParamUnchecked</a></code> </p>
+ </td>
+ <td><p>Set a parameter UNCHECKED</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="showPP.html">showPP</a></code> </p>
+ </td>
+ <td><p>Show pretty print</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="simpleEstimate.html">simpleEstimate</a></code> </p>
+ </td>
+ <td><p>Estimate simple simulation parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>The SimpleParams class</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="simpleSimulate.html">simpleSimulate</a></code> </p>
+ </td>
+ <td><p>Simple simulation</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatEstBCV.html">splatEstBCV</a></code> </p>
+ </td>
+ <td><p>Estimate Splat Biological Coefficient of Variation parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatEstDropout.html">splatEstDropout</a></code> </p>
+ </td>
+ <td><p>Estimate Splat dropout parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatEstimate.html">splatEstimate</a></code> </p>
+ </td>
+ <td><p>Estimate Splat simulation parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatEstLib.html">splatEstLib</a></code> </p>
+ </td>
+ <td><p>Estimate Splat library size parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatEstMean.html">splatEstMean</a></code> </p>
+ </td>
+ <td><p>Estimate Splat mean parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatEstOutlier.html">splatEstOutlier</a></code> </p>
+ </td>
+ <td><p>Estimate Splat expression outlier parameters</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>The SplatParams class</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimBatchCellMeans.html">splatSimBatchCellMeans</a></code> </p>
+ </td>
+ <td><p>Simulate batch means</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimBatchEffects.html">splatSimBatchEffects</a></code> </p>
+ </td>
+ <td><p>Simulate batch effects</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimBCVMeans.html">splatSimBCVMeans</a></code> </p>
+ </td>
+ <td><p>Simulate BCV means</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimCellMeans.html">splatSimSingleCellMeans</a></code> <code><a href="splatSimCellMeans.html">splatSimGroupCellMeans</a></code> <code><a href="splatSimCellMeans.html">splatSimPathCellMeans</a></code> </p>
+ </td>
+ <td><p>Simulate cell means</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimDE.html">splatSimGroupDE</a></code> <code><a href="splatSimDE.html">splatSimPathDE</a></code> </p>
+ </td>
+ <td><p>Simulate group differential expression</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimDropout.html">splatSimDropout</a></code> </p>
+ </td>
+ <td><p>Simulate dropout</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimGeneMeans.html">splatSimGeneMeans</a></code> </p>
+ </td>
+ <td><p>Simulate gene means</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimLibSizes.html">splatSimLibSizes</a></code> </p>
+ </td>
+ <td><p>Simulate library sizes</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimTrueCounts.html">splatSimTrueCounts</a></code> </p>
+ </td>
+ <td><p>Simulate true counts</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="splatSimulate.html">splatSimulate</a></code> <code><a href="splatSimulate.html">splatSimulateSingle</a></code> <code><a href="splatSimulate.html">splatSimulateGroups</a></code> <code><a href="splatSimulate.html">splatSimulatePaths</a></code> </p>
+ </td>
+ <td><p>Splat simulation</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p></p>
+ </td>
+ <td><p>splatter.</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="summariseDiff.html">summariseDiff</a></code> </p>
+ </td>
+ <td><p>Summarise diffSCESets</p></td>
+ </tr><tr>
+ <!-- -->
+ <td>
+ <p><code><a href="winsorize.html">winsorize</a></code> </p>
+ </td>
+ <td><p>Winsorize vector</p></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#section-all-functions">All functions</a></li>
+ </ul>
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
new file mode 100644
index 0000000000000000000000000000000000000000..85edb2cd93551a76bee0f4ee5f285c2f7aadaca5
--- /dev/null
+++ b/docs/reference/listSims.html
@@ -0,0 +1,176 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>List simulations — listSims • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>List simulations</h1>
+ </div>
+
+
+ <p>List all the simulations that are currently available in Splatter with a
+brief description.</p>
+
+
+ <pre class="usage"><span class='fu'>listSims</span>(<span class='kw'>print</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>print</th>
+ <td><p>logical. Whether to print to the console.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Invisibly returns a data.frame containing the information that is
+displayed.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>listSims</span>()</div><div class='output co'>#> Splatter currently contains 8 simulations
+#>
+#> Splat (splat)
+#> DOI: Github:
+#> The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout can be optionally added.
+#>
+#> Splat Single (splatSingle)
+#> DOI: Github:
+#> The Splat simulation with a single population.
+#>
+#> Splat Groups (splatGroups)
+#> DOI: Github:
+#> The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution.
+#>
+#> Splat Paths (splatPaths)
+#> DOI: Github:
+#> The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways.
+#>
+#> Simple (simple)
+#> DOI: Github:
+#> A simple simulation with gamma means and negative binomial counts.
+#>
+#> Lun (lun)
+#> DOI: 10.1186/s13059-016-0947-7 Github: MarioniLab/Deconvolution2016
+#> Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.
+#>
+#> Lun 2 (lun2)
+#> DOI: 10.1101/073973 Github: MarioniLab/PlateEffects2016
+#> Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.
+#>
+#> scDD (scDD)
+#> DOI: 10.1186/s13059-016-1077-y Github: kdkorthauer/scDD
+#> The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/logistic.html b/docs/reference/logistic.html
new file mode 100644
index 0000000000000000000000000000000000000000..7e3087b15682a753f4a71b4aa754db40a6adc9a4
--- /dev/null
+++ b/docs/reference/logistic.html
@@ -0,0 +1,145 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Logistic function — logistic • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Logistic function</h1>
+ </div>
+
+
+ <p>Implementation of the logistic function</p>
+
+
+ <pre class="usage"><span class='fu'>logistic</span>(<span class='no'>x</span>, <span class='no'>x0</span>, <span class='no'>k</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>value to apply the function to.</p></td>
+ </tr>
+ <tr>
+ <th>x0</th>
+ <td><p>midpoint parameter. Gives the centre of the function.</p></td>
+ </tr>
+ <tr>
+ <th>k</th>
+ <td><p>shape parameter. Gives the slope of the function.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Value of logistic funciton with given parameters</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/lun2Estimate.html b/docs/reference/lun2Estimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..bd99ded655c30676ce7b4be1221fa55cf75c25ba
--- /dev/null
+++ b/docs/reference/lun2Estimate.html
@@ -0,0 +1,186 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Lun2 simulation parameters — lun2Estimate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Lun2 simulation parameters</h1>
+ </div>
+
+
+ <p>Estimate simulation parameters for the Lun2 simulation from a real dataset.</p>
+
+
+ <pre class="usage"><span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>,
+ <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
+
+<span class='co'># S3 method for SCESet</span>
+<span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(),
+ <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
+
+<span class='co'># S3 method for matrix</span>
+<span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(),
+ <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>either a counts matrix or an SCESet object containing count
+data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>plates</th>
+ <td><p>integer vector giving the plate that each cell originated from.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>Lun2Params object to store estimated values in.</p></td>
+ </tr>
+ <tr>
+ <th>min.size</th>
+ <td><p>minimum size of clusters when identifying group of cells in
+the data.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to show progress messages.</p></td>
+ </tr>
+ <tr>
+ <th>BPPARAM</th>
+ <td><p>A <code><a href='http://www.rdocumentation.org/packages/BiocParallel/topics/BiocParallelParam-class'>BiocParallelParam</a></code> instance
+giving the parallel back-end to be used. Default is
+<code><a href='http://www.rdocumentation.org/packages/BiocParallel/topics/SerialParam-class'>SerialParam</a></code> which uses a single core.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>LunParams object containing the estimated parameters.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>See <code><a href='Lun2Params.html'>Lun2Params</a></code> for more details on the parameters.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'>data</span>(<span class='st'>"sc_example_cell_info"</span>)
+<span class='no'>plates</span> <span class='kw'><-</span> <span class='fu'>factor</span>(<span class='no'>sc_example_cell_info</span>$<span class='no'>Mutation_Status</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lun2Estimate</span>(<span class='no'>sc_example_counts</span>, <span class='no'>plates</span>, <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>20</span>)
+<span class='no'>params</span>
+<span class='co'># }</span></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
new file mode 100644
index 0000000000000000000000000000000000000000..71cd9f42667dcfa51b6d4aee5bfc35de6ec68190
--- /dev/null
+++ b/docs/reference/lun2Simulate.html
@@ -0,0 +1,183 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Lun2 simulation — lun2Simulate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Lun2 simulation</h1>
+ </div>
+
+
+ <p>Simulate single-cell RNA-seq count data using the method described in Lun
+and Marioni "Overcoming confounding plate effects in differential expression
+analyses of single-cell RNA-seq data".</p>
+
+
+ <pre class="usage"><span class='fu'>lun2Simulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>zinb</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>Lun2Params object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>zinb</th>
+ <td><p>logical. Whether to use a zero-inflated model.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet containing simulated counts.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The Lun2 simulation uses a negative-binomial distribution where the means and
+dispersions have been sampled from a real dataset
+(using <code><a href='lun2Estimate.html'>lun2Estimate</a></code>). The other core feature of the Lun2
+simulation is the addition of plate effects. Differential expression can be
+added between two groups of plates (an "ingroup" and all other plates).
+Library size factors are also applied and optionally a zero-inflated
+negative-binomial can be used.</p>
+<p>If the number of genes to simulate differs from the number of provied gene
+parameters or the number of cells to simulate differs from the number of
+library sizes the relevant paramters will be sampled with a warning. This
+allows any number of genes or cells to be simulated regardless of the
+number in the dataset used in the estimation step but has the downside that
+some genes or cells may be simulated multiple times.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Lun ATL, Marioni JC. Overcoming confounding plate effects in differential
+expression analyses of single-cell RNA-seq data. bioRxiv (2016).</p>
+<p>Paper: <a href='dx.doi.org/10.1101/073973'>dx.doi.org/10.1101/073973</a></p>
+<p>Code: <a href='https://github.com/MarioniLab/PlateEffects2016'>https://github.com/MarioniLab/PlateEffects2016</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>lun2Simulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Simulating plate means...</span></div><div class='output co'>#> <span class='message'>Simulating libray size factors...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='output co'>#> <span class='message'>Done!</span></div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..d627d3d46ddd252d3fde96c4fe36f5a5e097674b
--- /dev/null
+++ b/docs/reference/lunEstimate.html
@@ -0,0 +1,186 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Lun simulation parameters — lunEstimate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Lun simulation parameters</h1>
+ </div>
+
+
+ <p>Estimate simulation parameters for the Lun simulation from a real dataset.</p>
+
+
+ <pre class="usage"><span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())
+
+<span class='co'># S3 method for SCESet</span>
+<span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())
+
+<span class='co'># S3 method for matrix</span>
+<span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>either a counts matrix or an SCESet object containing count
+data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>LunParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>LunParams object containing the estimated parameters.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
+input data. No other parameters are estimated. See <code><a href='LunParams.html'>LunParams</a></code>
+for more details on the parameters.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lunEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class LunParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 40 298310
+#>
+#> 9 additional parameters
+#>
+#> Mean:
+#> [Rate] [Shape]
+#> 2 2
+#>
+#> Counts:
+#> [Dispersion]
+#> 0.1
+#>
+#> Groups:
+#> [Groups] [GROUP CELLS]
+#> 1 40
+#>
+#> Diff expr:
+#> [Genes] [Up Prop] [Up FC] [Down FC]
+#> 1000 0.5 5 0
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/lunSimulate.html b/docs/reference/lunSimulate.html
new file mode 100644
index 0000000000000000000000000000000000000000..eb4f1814a24fb546e71eaaa9ac5a46a7fa82795b
--- /dev/null
+++ b/docs/reference/lunSimulate.html
@@ -0,0 +1,175 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Lun simulation — lunSimulate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Lun simulation</h1>
+ </div>
+
+
+ <p>Simulate single-cell RNA-seq count data using the method described in Lun,
+Bach and Marioni "Pooling across cells to normalize single-cell RNA
+sequencing data with many zero counts".</p>
+
+
+ <pre class="usage"><span class='fu'>lunSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>LunParams object containing Lun simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet object containing the simulated counts and intermediate
+values.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The Lun simulation generates gene mean expression levels from a gamma
+distribution with <code>shape = mean.shape</code> and <code>rate = mean.rate</code>.
+Counts are then simulated from a negative binomial distribution with
+<code>mu = means</code> and <code>size = 1 / bcv.common</code>. In addition each cell is
+given a size factor (<code>2 ^ rnorm(nCells, mean = 0, sd = 0.5)</code>) and
+differential expression can be simulated with fixed fold changes.</p>
+<p>See <code><a href='LunParams.html'>LunParams</a></code> for details of the parameters.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Lun ATL, Bach K, Marioni JC. Pooling across cells to normalize single-cell
+RNA sequencing data with many zero counts. Genome Biology (2016).</p>
+<p>Paper: <a href='dx.doi.org/10.1186/s13059-016-0947-7'>dx.doi.org/10.1186/s13059-016-0947-7</a></p>
+<p>Code: <a href='https://github.com/MarioniLab/Deconvolution2016'>https://github.com/MarioniLab/Deconvolution2016</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>lunSimulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='input'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/makeCompPanel.html b/docs/reference/makeCompPanel.html
new file mode 100644
index 0000000000000000000000000000000000000000..5cc75f0d1f83a5628287cfb8f713264a97ed8473
--- /dev/null
+++ b/docs/reference/makeCompPanel.html
@@ -0,0 +1,157 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Make comparison panel — makeCompPanel • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Make comparison panel</h1>
+ </div>
+
+
+ <p>Combine the plots from <code>compareSCESets</code> into a single panel.</p>
+
+
+ <pre class="usage"><span class='fu'>makeCompPanel</span>(<span class='no'>comp</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>,
+ <span class='st'>"Mean-variance relationship"</span>, <span class='st'>"Library size"</span>, <span class='st'>"Zeros per gene"</span>,
+ <span class='st'>"Zeros per cell"</span>, <span class='st'>"Mean-zeros relationship"</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>comp</th>
+ <td><p>list returned by <code><a href='compareSCESets.html'>compareSCESets</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>title</th>
+ <td><p>title for the panel.</p></td>
+ </tr>
+ <tr>
+ <th>labels</th>
+ <td><p>vector of labels for each of the seven plots.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Combined panel plot</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
+<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
+<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'><a href='compareSCESets.html'>compareSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='no'>panel</span> <span class='kw'><-</span> <span class='fu'>makeCompPanel</span>(<span class='no'>comparison</span>)
+<span class='co'># }</span><div class='input'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
new file mode 100644
index 0000000000000000000000000000000000000000..49746d88248b9bd8d08ca01755c393541c29d35c
--- /dev/null
+++ b/docs/reference/makeDiffPanel.html
@@ -0,0 +1,157 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Make difference panel — makeDiffPanel • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Make difference panel</h1>
+ </div>
+
+
+ <p>Combine the plots from <code>diffSCESets</code> into a single panel.</p>
+
+
+ <pre class="usage"><span class='fu'>makeDiffPanel</span>(<span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Difference comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>,
+ <span class='st'>"Variance"</span>, <span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>, <span class='st'>"Zeros per gene"</span>,
+ <span class='st'>"Mean-variance relationship"</span>, <span class='st'>"Mean-zeros relationship"</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>diff</th>
+ <td><p>list returned by <code><a href='diffSCESets.html'>diffSCESets</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>title</th>
+ <td><p>title for the panel.</p></td>
+ </tr>
+ <tr>
+ <th>labels</th>
+ <td><p>vector of labels for each of the seven sections.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Combined panel plot</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
+<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
+<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCESets.html'>diffSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>panel</span> <span class='kw'><-</span> <span class='fu'>makeDiffPanel</span>(<span class='no'>difference</span>)
+<span class='co'># }</span><div class='input'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
new file mode 100644
index 0000000000000000000000000000000000000000..0b998d0e8a77eb55e88194325e8307007502368c
--- /dev/null
+++ b/docs/reference/makeOverallPanel.html
@@ -0,0 +1,164 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Make overall panel — makeOverallPanel • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Make overall panel</h1>
+ </div>
+
+
+ <p>Combine the plots from <code>compSCESets</code> and <code>diffSCESets</code> into a
+single panel.</p>
+
+
+ <pre class="usage"><span class='fu'>makeOverallPanel</span>(<span class='no'>comp</span>, <span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Overall comparison"</span>,
+ <span class='kw'>row.labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Mean-variance relationship"</span>,
+ <span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>, <span class='st'>"Zeros per gene"</span>,
+ <span class='st'>"Mean-zeros relationship"</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>comp</th>
+ <td><p>list returned by <code><a href='compareSCESets.html'>compareSCESets</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>diff</th>
+ <td><p>list returned by <code><a href='diffSCESets.html'>diffSCESets</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>title</th>
+ <td><p>title for the panel.</p></td>
+ </tr>
+ <tr>
+ <th>row.labels</th>
+ <td><p>vector of labels for each of the seven rows.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Combined panel plot</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
+<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
+<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compSCESets</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCESets.html'>diffSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>panel</span> <span class='kw'><-</span> <span class='fu'>makeOverallPanel</span>(<span class='no'>comparison</span>, <span class='no'>difference</span>)
+<span class='co'># }</span><div class='input'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..20df2fac2c9871ee591feeacb181d3ad070a0d4a
--- /dev/null
+++ b/docs/reference/newParams.html
@@ -0,0 +1,151 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>New Params — newParams • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>New Params</h1>
+ </div>
+
+
+ <p>Create a new Params object. Functions exist for each of the different
+Params subtypes.</p>
+
+
+ <pre class="usage"><span class='fu'>newLun2Params</span>(<span class='no'>...</span>)
+
+<span class='fu'>newLunParams</span>(<span class='no'>...</span>)
+
+<span class='fu'>newSCDDParams</span>(<span class='no'>...</span>)
+
+<span class='fu'>newSimpleParams</span>(<span class='no'>...</span>)
+
+<span class='fu'>newSplatParams</span>(<span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>...</th>
+ <td><p>additional parameters passed to <code><a href='setParams.html'>setParams</a></code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>New Params object.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>newSimpleParams</span>()
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>newSimpleParams</span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>200</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/rbindMatched.html b/docs/reference/rbindMatched.html
new file mode 100644
index 0000000000000000000000000000000000000000..e33224bb7335882692696684360bb0004f7944c1
--- /dev/null
+++ b/docs/reference/rbindMatched.html
@@ -0,0 +1,143 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Bind rows (matched) — rbindMatched • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Bind rows (matched)</h1>
+ </div>
+
+
+ <p>Bind the rows of two data frames, keeping only the columns that are common
+to both.</p>
+
+
+ <pre class="usage"><span class='fu'>rbindMatched</span>(<span class='no'>df1</span>, <span class='no'>df2</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>df1</th>
+ <td><p>first data.frame to bind.</p></td>
+ </tr>
+ <tr>
+ <th>df2</th>
+ <td><p>second data.frame to bind.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>data.frame containing rows from <code>df1</code> and <code>df2</code> but only
+ common columns.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..d1c94f1b62e3edd95c3adcee4a51da23b8ce7d8c
--- /dev/null
+++ b/docs/reference/scDDEstimate.html
@@ -0,0 +1,184 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate scDD simulation parameters — scDDEstimate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate scDD simulation parameters</h1>
+ </div>
+
+
+ <p>Estimate simulation parameters for the scDD simulation from a real dataset.</p>
+
+
+ <pre class="usage"><span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
+
+<span class='co'># S3 method for SCESet</span>
+<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(),
+ <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
+
+<span class='co'># S3 method for matrix</span>
+<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(),
+ <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>either a counts matrix or an SCESet object containing count
+data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>conditions</th>
+ <td><p>Vector giving the condition that each cell belongs to.
+Conditions can be 1 or 2.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SCDDParams object to store estimated values in.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to show progress messages.</p></td>
+ </tr>
+ <tr>
+ <th>BPPARAM</th>
+ <td><p>A <code><a href='http://www.rdocumentation.org/packages/BiocParallel/topics/BiocParallelParam-class'>BiocParallelParam</a></code> instance
+giving the parallel back-end to be used. Default is
+<code><a href='http://www.rdocumentation.org/packages/BiocParallel/topics/SerialParam-class'>SerialParam</a></code> which uses a single core.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCDDParams object containing the estimated parameters.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function applies <code><a href='http://www.rdocumentation.org/packages/scDD/topics/preprocess'>preprocess</a></code> to the counts then uses
+<code><a href='http://www.rdocumentation.org/packages/scDD/topics/scDD'>scDD</a></code> to estimate the numbers of each gene type to
+simulate. The output is then converted to a SCDDParams object. See
+<code><a href='http://www.rdocumentation.org/packages/scDD/topics/preprocess'>preprocess</a></code> and <code><a href='http://www.rdocumentation.org/packages/scDD/topics/scDD'>scDD</a></code> for details.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='no'>conditions</span> <span class='kw'><-</span> <span class='fu'>sample</span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'>ncol</span>(<span class='no'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>scDDEstimate</span>(<span class='no'>sc_example_counts</span>, <span class='no'>conditions</span>)
+<span class='no'>params</span>
+<span class='co'># }</span></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
new file mode 100644
index 0000000000000000000000000000000000000000..59f655fa2688efa106c50028b33358e02f31c510
--- /dev/null
+++ b/docs/reference/scDDSimulate.html
@@ -0,0 +1,187 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>scDD simulation — scDDSimulate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>scDD simulation</h1>
+ </div>
+
+
+ <p>Simulate counts using the scDD method.</p>
+
+
+ <pre class="usage"><span class='fu'>scDDSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>plots</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>plot.file</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>SCDDParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>plots</th>
+ <td><p>logical. whether to generate scDD fold change and validation
+plots.</p></td>
+ </tr>
+ <tr>
+ <th>plot.file</th>
+ <td><p>File path to save plots as PDF.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ <tr>
+ <th>BPPARAM</th>
+ <td><p>A <code><a href='http://www.rdocumentation.org/packages/BiocParallel/topics/BiocParallelParam-class'>BiocParallelParam</a></code> instance
+giving the parallel back-end to be used. Default is
+<code><a href='http://www.rdocumentation.org/packages/BiocParallel/topics/SerialParam-class'>SerialParam</a></code> which uses a single core.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet containing simulated counts</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> that
+takes a <code><a href='SCDDParams.html'>SCDDParams</a></code>, runs the simulation then converts the
+output to an <code><a href='http://www.rdocumentation.org/packages/scater/topics/SCESet'>SCESet</a></code> object. See
+<code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> for more details of how the simulation works.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Korthauer KD, Chu L-F, Newton MA, Li Y, Thomson J, Stewart R, et al. A
+statistical approach for identifying differential distributions in
+single-cell RNA-seq experiments. Genome Biology (2016).</p>
+<p>Paper: <a href='10.1186/s13059-016-1077-y'>10.1186/s13059-016-1077-y</a></p>
+<p>Code: <a href='https://github.com/kdkorthauer/scDD'>https://github.com/kdkorthauer/scDD</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>scDDSimulate</span>()
+<span class='co'># }</span></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
new file mode 100644
index 0000000000000000000000000000000000000000..75c292d597425b1c74624f786fd609c69c96d3d9
--- /dev/null
+++ b/docs/reference/setParam.html
@@ -0,0 +1,182 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Set a parameter — setParam • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Set a parameter</h1>
+ </div>
+
+
+ <p>Function for setting parameter values.</p>
+
+
+ <pre class="usage"><span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
+<span class='co'># S4 method for Lun2Params</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
+<span class='co'># S4 method for LunParams</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
+<span class='co'># S4 method for Params</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
+<span class='co'># S4 method for SCDDParams</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
+<span class='co'># S4 method for SplatParams</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>object to set parameter in.</p></td>
+ </tr>
+ <tr>
+ <th>name</th>
+ <td><p>name of the parameter to set.</p></td>
+ </tr>
+ <tr>
+ <th>value</th>
+ <td><p>value to set the paramter to.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Object with new parameter value.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
+<span class='fu'>setParam</span>(<span class='no'>params</span>, <span class='st'>"nGenes"</span>, <span class='fl'>100</span>)</div><div class='output co'>#> A Params object of class SimpleParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (GENES) (Cells) [Seed]
+#> 100 100 298310
+#>
+#> 3 additional parameters
+#>
+#> Mean:
+#> (Rate) (Shape)
+#> 0.3 0.4
+#>
+#> Counts:
+#> [Dispersion]
+#> 0.1
+#> </div><div class='input'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/setParamUnchecked.html b/docs/reference/setParamUnchecked.html
new file mode 100644
index 0000000000000000000000000000000000000000..d13ef8311c49c1d2b5f60f824700b03424c70c0f
--- /dev/null
+++ b/docs/reference/setParamUnchecked.html
@@ -0,0 +1,149 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Set a parameter UNCHECKED — setParamUnchecked • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Set a parameter UNCHECKED</h1>
+ </div>
+
+
+ <p>Function for setting parameter values. THE OUTPUT IS NOT CHECKED FOR
+VALIDITY!</p>
+
+
+ <pre class="usage"><span class='fu'>setParamUnchecked</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
+<span class='co'># S4 method for Params</span>
+<span class='fu'>setParamUnchecked</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>object to set parameter in.</p></td>
+ </tr>
+ <tr>
+ <th>name</th>
+ <td><p>name of the parameter to set.</p></td>
+ </tr>
+ <tr>
+ <th>value</th>
+ <td><p>value to set the paramter to.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Object with new parameter value.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..4ebe0bfad70498c77ee2962f0272375cabd15e41
--- /dev/null
+++ b/docs/reference/setParams.html
@@ -0,0 +1,214 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Set parameters — setParams • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Set parameters</h1>
+ </div>
+
+
+ <p>Set multiple parameters in a Params object.</p>
+
+
+ <pre class="usage"><span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>Params object to set parameters in.</p></td>
+ </tr>
+ <tr>
+ <th>update</th>
+ <td><p>list of parameters to set where <code>names(update)</code> are the
+names of the parameters to set and the items in the list are values.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>additional parameters to set. These are combined with any
+parameters specified in <code>update</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Params object with updated values.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Each parameter is set by a call to <code><a href='setParam.html'>setParam</a></code>. If the same
+parameter is specified multiple times it will be set multiple times.
+Parameters can be specified using a list via <code>update</code> (useful when
+collecting parameter values in some way) or individually (useful when setting
+them manually), see examples.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (Genes) (Cells) [Seed]
+#> 10000 100 298310
+#>
+#> 3 additional parameters
+#>
+#> Mean:
+#> (Rate) (Shape)
+#> 0.3 0.4
+#>
+#> Counts:
+#> [Dispersion]
+#> 0.1
+#> </div><div class='input'><span class='co'># Set individually</span>
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>50</span>)
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 1000 50 298310
+#>
+#> 3 additional parameters
+#>
+#> Mean:
+#> (Rate) (Shape)
+#> 0.3 0.4
+#>
+#> Counts:
+#> [Dispersion]
+#> 0.1
+#> </div><div class='input'><span class='co'># Set via update list</span>
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='fu'>list</span>(<span class='kw'>mean.rate</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>mean.shape</span> <span class='kw'>=</span> <span class='fl'>0.8</span>))
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 1000 50 298310
+#>
+#> 3 additional parameters
+#>
+#> Mean:
+#> (RATE) (SHAPE)
+#> 0.2 0.8
+#>
+#> Counts:
+#> [Dispersion]
+#> 0.1
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/setParamsUnchecked.html b/docs/reference/setParamsUnchecked.html
new file mode 100644
index 0000000000000000000000000000000000000000..cbafc76deea8e479a7d6ca5b615cf353049a130f
--- /dev/null
+++ b/docs/reference/setParamsUnchecked.html
@@ -0,0 +1,157 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Set parameters UNCHECKED — setParamsUnchecked • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Set parameters UNCHECKED</h1>
+ </div>
+
+
+ <p>Set multiple parameters in a Params object.</p>
+
+
+ <pre class="usage"><span class='fu'>setParamsUnchecked</span>(<span class='no'>params</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>Params object to set parameters in.</p></td>
+ </tr>
+ <tr>
+ <th>update</th>
+ <td><p>list of parameters to set where <code>names(update)</code> are the
+names of the parameters to set and the items in the list are values.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>additional parameters to set. These are combined with any
+parameters specified in <code>update</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Params object with updated values.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Each parameter is set by a call to <code><a href='setParam.html'>setParam</a></code>. If the same
+parameter is specified multiple times it will be set multiple times.
+Parameters can be specified using a list via <code>update</code> (useful when
+collecting parameter values in some way) or individually (useful when setting
+them manually), see examples. THE FINAL OBJECT IS NOT CHECKED FOR VALIDITY!</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/showPP.html b/docs/reference/showPP.html
new file mode 100644
index 0000000000000000000000000000000000000000..8b1bbc2b814455013d5f0b2b806a1f12c97e21b6
--- /dev/null
+++ b/docs/reference/showPP.html
@@ -0,0 +1,141 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Show pretty print — showPP • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Show pretty print</h1>
+ </div>
+
+
+ <p>Function used for pretty printing params object.</p>
+
+
+ <pre class="usage"><span class='fu'>showPP</span>(<span class='no'>params</span>, <span class='no'>pp</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>object to show.</p></td>
+ </tr>
+ <tr>
+ <th>pp</th>
+ <td><p>list specifying how the object should be displayed.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Print params object to console</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..e62c415e5b3072c5e5f054dfee0757fcaa0edebf
--- /dev/null
+++ b/docs/reference/simpleEstimate.html
@@ -0,0 +1,180 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate simple simulation parameters — simpleEstimate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate simple simulation parameters</h1>
+ </div>
+
+
+ <p>Estimate simulation parameters for the simple simulation from a real dataset.</p>
+
+
+ <pre class="usage"><span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())
+
+<span class='co'># S3 method for SCESet</span>
+<span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())
+
+<span class='co'># S3 method for matrix</span>
+<span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>either a counts matrix or an SCESet object containing count
+data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SimpleParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SimpleParams object containing the estimated parameters.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
+input data. The mean parameters are estimated by fitting a gamma distribution
+to the library size normalised mean expression level using
+<code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>. See <code><a href='SimpleParams.html'>SimpleParams</a></code> for more
+details on the parameters.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>simpleEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 40 298310
+#>
+#> 3 additional parameters
+#>
+#> Mean:
+#> (RATE) (SHAPE)
+#> 0.0008052293183292 0.131835949613878
+#>
+#> Counts:
+#> [Dispersion]
+#> 0.1
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/simpleSimulate.html b/docs/reference/simpleSimulate.html
new file mode 100644
index 0000000000000000000000000000000000000000..aae3d8b90da9929b3477bc65c8e8dbde6b8b2067
--- /dev/null
+++ b/docs/reference/simpleSimulate.html
@@ -0,0 +1,162 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simple simulation — simpleSimulate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simple simulation</h1>
+ </div>
+
+
+ <p>Simulate counts from a simple negative binomial distribution without
+simulated library sizes, differential expression etc.</p>
+
+
+ <pre class="usage"><span class='fu'>simpleSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>SimpleParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet containing simulated counts</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Gene means are simulated from a gamma distribution with
+<code>shape = mean.shape</code> and <code>rate = mean.rate</code>. Counts are then
+simulated from a negative binomial distribution with <code>mu = means</code> and
+<code>size = 1 / counts.disp</code>. See <code><a href='SimpleParams.html'>SimpleParams</a></code> for more
+details of the parameters.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>simpleSimulate</span>()</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='co'># Override default parameters</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>simpleSimulate</span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatEstBCV.html b/docs/reference/splatEstBCV.html
new file mode 100644
index 0000000000000000000000000000000000000000..a6f8dabb5a6731705c1e1fb36fc4bcd054d729e6
--- /dev/null
+++ b/docs/reference/splatEstBCV.html
@@ -0,0 +1,153 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Splat Biological Coefficient of Variation parameters — splatEstBCV • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Splat Biological Coefficient of Variation parameters</h1>
+ </div>
+
+
+ <p>Parameters are estimated using the <code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function
+in the <code>edgeR</code> package.</p>
+
+
+ <pre class="usage"><span class='fu'>splatEstBCV</span>(<span class='no'>counts</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>counts matrix to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SplatParams object with estimated values.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The <code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function is used to estimate the common
+dispersion and prior degrees of freedom. See
+<code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> for details. When estimating parameters on
+simulated data we found a broadly linear relationship between the true
+underlying common dispersion and the <code>edgR</code> estimate, therefore we
+apply a small correction, <code>disp = 0.1 + 0.25 * edgeR.disp</code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatEstDropout.html b/docs/reference/splatEstDropout.html
new file mode 100644
index 0000000000000000000000000000000000000000..e129a2566a20c8957229bd596ca5425fe4e658af
--- /dev/null
+++ b/docs/reference/splatEstDropout.html
@@ -0,0 +1,150 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Splat dropout parameters — splatEstDropout • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Splat dropout parameters</h1>
+ </div>
+
+
+ <p>Estimate the midpoint and shape parameters for the logistic function used
+when simulating dropout.</p>
+
+
+ <pre class="usage"><span class='fu'>splatEstDropout</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>norm.counts</th>
+ <td><p>library size normalised counts matrix.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SplatParams object with estimated values.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Logistic function parameters are estimated by fitting a logistic function
+to the relationship between log2 mean gene expression and the proportion of
+zeros in each gene. See <code><a href='http://www.rdocumentation.org/packages/stats/topics/nls'>nls</a></code> for details of fitting.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatEstLib.html b/docs/reference/splatEstLib.html
new file mode 100644
index 0000000000000000000000000000000000000000..c18875d89112c0780e37f4bdd23a287f92c233b8
--- /dev/null
+++ b/docs/reference/splatEstLib.html
@@ -0,0 +1,143 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Splat library size parameters — splatEstLib • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Splat library size parameters</h1>
+ </div>
+
+
+ <p>A log-normal distribution is fitted to the library sizes and the estimated
+parameters are added to the params object. See
+<code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code> for details on the fitting.</p>
+
+
+ <pre class="usage"><span class='fu'>splatEstLib</span>(<span class='no'>counts</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>counts matrix to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>splatParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>splatParams object with estimated values.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatEstMean.html b/docs/reference/splatEstMean.html
new file mode 100644
index 0000000000000000000000000000000000000000..78ff079a9dc00296953a945a752a22a05d4697ec
--- /dev/null
+++ b/docs/reference/splatEstMean.html
@@ -0,0 +1,154 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Splat mean parameters — splatEstMean • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Splat mean parameters</h1>
+ </div>
+
+
+ <p>Estimate rate and shape parameters for the gamma distribution used to
+simulate gene expression means.</p>
+
+
+ <pre class="usage"><span class='fu'>splatEstMean</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>norm.counts</th>
+ <td><p>library size normalised counts matrix.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SplatParams object with estimated values.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Parameter for the gamma distribution are estimated by fitting the mean
+normalised counts using <code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>. The 'maximum
+goodness-of-fit estimation' method is used to minimise the Cramer-von Mises
+distance. This can fail in some situations, in which case the 'method of
+moments estimation' method is used instead. Prior to fitting the means are
+winsorized by setting the top and bottom 10 percent of values to the 10th
+and 90th percentiles.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatEstOutlier.html b/docs/reference/splatEstOutlier.html
new file mode 100644
index 0000000000000000000000000000000000000000..0df72e4f77872ee97c31f442dfdd5dd7e989fa18
--- /dev/null
+++ b/docs/reference/splatEstOutlier.html
@@ -0,0 +1,155 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Splat expression outlier parameters — splatEstOutlier • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Splat expression outlier parameters</h1>
+ </div>
+
+
+ <p>Parameters are estimated by comparing means of individual genes to the
+median mean expression level.</p>
+
+
+ <pre class="usage"><span class='fu'>splatEstOutlier</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>norm.counts</th>
+ <td><p>library size normalised counts matrix.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SplatParams object with estimated values.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Expression outlier genes are detected using the Median Absolute Deviation
+(MAD) from median method. If the log2 mean expression of a gene is greater
+than two MADs above the median log2 mean expression it is designated as an
+outlier. The proportion of outlier genes is used to estimate the outlier
+probability. Factors for each outlier gene are calculated by dividing mean
+expression by the median mean expression. A log-normal distribution is then
+fitted to these factors in order to estimate the outlier factor location and
+scale parameters using <code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..1d48ca737e7fbc7173cd6ad85677dede84b09977
--- /dev/null
+++ b/docs/reference/splatEstimate.html
@@ -0,0 +1,208 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Splat simulation parameters — splatEstimate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Splat simulation parameters</h1>
+ </div>
+
+
+ <p>Estimate simulation parameters for the Splat simulation from a real
+dataset. See the individual estimation functions for more details on how this
+is done.</p>
+
+
+ <pre class="usage"><span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())
+
+<span class='co'># S3 method for SCESet</span>
+<span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())
+
+<span class='co'># S3 method for matrix</span>
+<span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>either a counts matrix or an SCESet object containing count
+data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object to store estimated values in.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SplatParams object containing the estimated parameters.</p>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p><code><a href='splatEstMean.html'>splatEstMean</a></code>, <code><a href='splatEstLib.html'>splatEstLib</a></code>,
+<code><a href='splatEstOutlier.html'>splatEstOutlier</a></code>, <code><a href='splatEstBCV.html'>splatEstBCV</a></code>,
+<code><a href='splatEstDropout.html'>splatEstDropout</a></code></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>splatEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class SplatParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 40 298310
+#>
+#> 27 additional parameters
+#>
+#> Batches:
+#> [Batches] [BATCH CELLS] [Location] [Scale]
+#> 1 40 0.1 0.1
+#>
+#> Mean:
+#> (RATE) (SHAPE)
+#> 0.0032639148887191 0.419304527025529
+#>
+#> Library size:
+#> (LOCATION) (SCALE)
+#> 12.7053037408488 0.58910919018286
+#>
+#> Exprs outliers:
+#> (PROBABILITY) (LOCATION) (SCALE)
+#> 0.00623376623376623 4.22280669039478 0.422108697251885
+#>
+#> Groups:
+#> [Groups] [Group Probs]
+#> 1 1
+#>
+#> Diff expr:
+#> [Probability] [Down Prob] [Location] [Scale]
+#> 0.1 0.5 0.1 0.4
+#>
+#> BCV:
+#> (COMMON DISP) (DOF)
+#> 3.21969047393022 14.7262017878812
+#>
+#> Dropout:
+#> [Present] (MIDPOINT) (SHAPE)
+#> FALSE 5.00420976858168 -0.652889139821156
+#>
+#> Paths:
+#> [From] [Length] [Skew] [Non-linear] [Sigma Factor]
+#> 0 100 0.5 0.1 0.8
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#see-also">See also</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
new file mode 100644
index 0000000000000000000000000000000000000000..6bd1068d7c989271f6f710a56f1372cb5d3e3759
--- /dev/null
+++ b/docs/reference/splatSimBCVMeans.html
@@ -0,0 +1,143 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate BCV means — splatSimBCVMeans • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate BCV means</h1>
+ </div>
+
+
+ <p>Simulate means for each gene in each cell that are adjusted to follow a
+mean-variance trend using Biological Coefficient of Variation taken from
+and inverse gamma distribution.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimBCVMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add BCV means to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with simulated BCV means.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
new file mode 100644
index 0000000000000000000000000000000000000000..a581b4c95c06fd5587aa76ed628202341246610a
--- /dev/null
+++ b/docs/reference/splatSimBatchCellMeans.html
@@ -0,0 +1,142 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate batch means — splatSimBatchCellMeans • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate batch means</h1>
+ </div>
+
+
+ <p>Simulate a mean for each gene in each cell incorporating batch effect
+factors.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimBatchCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add batch means to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with simulated batch means.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
new file mode 100644
index 0000000000000000000000000000000000000000..8007b81ae776d1f02259764024689eed91db73ab
--- /dev/null
+++ b/docs/reference/splatSimBatchEffects.html
@@ -0,0 +1,143 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate batch effects — splatSimBatchEffects • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate batch effects</h1>
+ </div>
+
+
+ <p>Simulate batch effects. Batch effect factors for each batch are produced
+using <code><a href='getLNormFactors.html'>getLNormFactors</a></code> and these are added along with updated
+means for each batch.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimBatchEffects</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add batch effects to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with simulated batch effects.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
new file mode 100644
index 0000000000000000000000000000000000000000..dcf19321b5f6f2c6ee903161e07a9d2acd703434
--- /dev/null
+++ b/docs/reference/splatSimCellMeans.html
@@ -0,0 +1,149 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate cell means — splatSimCellMeans • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate cell means</h1>
+ </div>
+
+
+ <p>Simulate a gene by cell matrix giving the mean expression for each gene in
+each cell. Cells start with the mean expression for the group they belong to
+(when simulating groups) or cells are assigned the mean expression from a
+random position on the appropriate path (when simulating paths). The selected
+means are adjusted for each cell's expected library size.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimSingleCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)
+
+<span class='fu'>splatSimGroupCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)
+
+<span class='fu'>splatSimPathCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add cell means to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with added cell means.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimDE.html b/docs/reference/splatSimDE.html
new file mode 100644
index 0000000000000000000000000000000000000000..dcab6a530a4929f62e8a20b1af7cb57395c929e0
--- /dev/null
+++ b/docs/reference/splatSimDE.html
@@ -0,0 +1,146 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate group differential expression — splatSimDE • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate group differential expression</h1>
+ </div>
+
+
+ <p>Simulate differential expression. Differential expression factors for each
+group are produced using <code><a href='getLNormFactors.html'>getLNormFactors</a></code> and these are added
+along with updated means for each group. For paths care is taked to make sure
+they are simulated in the correct order.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimGroupDE</span>(<span class='no'>sim</span>, <span class='no'>params</span>)
+
+<span class='fu'>splatSimPathDE</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add differential expression to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>splatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with simulated differential expression.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimDropout.html b/docs/reference/splatSimDropout.html
new file mode 100644
index 0000000000000000000000000000000000000000..c7fdb3dbcf2eedf10dec19c9aee75938bc3a241b
--- /dev/null
+++ b/docs/reference/splatSimDropout.html
@@ -0,0 +1,144 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate dropout — splatSimDropout • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate dropout</h1>
+ </div>
+
+
+ <p>A logistic function is used to form a relationshop between the expression
+level of a gene and the probability of dropout, giving a probability for each
+gene in each cell. These probabilities are used in a Bernoulli distribution
+to decide which counts should be dropped.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimDropout</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add dropout to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with simulated dropout and observed counts.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
new file mode 100644
index 0000000000000000000000000000000000000000..662d14c87ef2cee5fd96170e0cfe05cb829584db
--- /dev/null
+++ b/docs/reference/splatSimGeneMeans.html
@@ -0,0 +1,143 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate gene means — splatSimGeneMeans • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate gene means</h1>
+ </div>
+
+
+ <p>Simulate gene means from a gamma distribution. Also simulates outlier
+expression factors. Genes with an outlier factor not equal to 1 are replaced
+with the median mean expression multiplied by the outlier factor.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimGeneMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add gene means to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with simulated gene means.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
new file mode 100644
index 0000000000000000000000000000000000000000..d5d12d2f314c20adf6be6829dd0ae26e06b168f0
--- /dev/null
+++ b/docs/reference/splatSimLibSizes.html
@@ -0,0 +1,141 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate library sizes — splatSimLibSizes • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate library sizes</h1>
+ </div>
+
+
+ <p>Simulate expected library sizes from a log-normal distribution</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimLibSizes</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add library size to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with simulated library sizes.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
new file mode 100644
index 0000000000000000000000000000000000000000..fd1e306d182e1553e1189c2783bb383db79d1d41
--- /dev/null
+++ b/docs/reference/splatSimTrueCounts.html
@@ -0,0 +1,143 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate true counts — splatSimTrueCounts • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate true counts</h1>
+ </div>
+
+
+ <p>Simulate a true counts matrix. Counts are simulated from a poisson
+distribution where Each gene in each cell has it's own mean based on the
+group (or path position), expected library size and BCV.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimTrueCounts</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SCESet to add true counts to.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object with simulation parameters.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet with simulated true counts.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
new file mode 100644
index 0000000000000000000000000000000000000000..77e480256988c6c9442137cd20ef910a4c8df896
--- /dev/null
+++ b/docs/reference/splatSimulate.html
@@ -0,0 +1,257 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Splat simulation — splatSimulate • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Splat simulation</h1>
+ </div>
+
+
+ <p>Simulate count data from a fictional single-cell RNA-seq experiment using
+the Splat method.</p>
+
+
+ <pre class="usage"><span class='fu'>splatSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"single"</span>, <span class='st'>"groups"</span>,
+ <span class='st'>"paths"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
+<span class='fu'>splatSimulateSingle</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
+<span class='fu'>splatSimulateGroups</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
+<span class='fu'>splatSimulatePaths</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>SplatParams object containing parameters for the simulation.
+See <code><a href='SplatParams.html'>SplatParams</a></code> for details.</p></td>
+ </tr>
+ <tr>
+ <th>method</th>
+ <td><p>which simulation method to use. Options are "single" which
+produces a single population, "groups" which produces distinct groups
+(eg. cell types) or "paths" which selects cells from continuous
+trajectories (eg. differentiation processes).</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SCESet object containing the simulated counts and intermediate
+values.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Parameters can be set in a variety of ways. If no parameters are provided
+the default parameters are used. Any parameters in <code>params</code> can be
+overridden by supplying additional arguments through a call to
+<code><a href='setParams.html'>setParams</a></code>. This design allows the user flexibility in
+how they supply parameters and allows small adjustments without creating a
+new <code>SplatParams</code> object. See examples for a demonstration of how this
+can be used.</p>
+<p>The simulation involves the following steps:</p><ol>
+<li><p>Set up simulation object</p></li>
+<li><p>Simulate library sizes</p></li>
+<li><p>Simulate gene means</p></li>
+<li><p>Simulate groups/paths</p></li>
+<li><p>Simulate BCV adjusted cell means</p></li>
+<li><p>Simulate true counts</p></li>
+<li><p>Simulate dropout</p></li>
+<li><p>Create final SCESet object</p></li>
+</ol>
+ <p>The final output is an <code><a href='http://www.rdocumentation.org/packages/scater/topics/SCESet'>SCESet</a></code> object that contains the
+simulated counts but also the values for various intermediate steps. These
+are stored in the <code><a href='http://www.rdocumentation.org/packages/Biobase/topics/phenoData'>phenoData</a></code> (for cell specific
+information), <code><a href='http://www.rdocumentation.org/packages/Biobase/topics/featureData'>featureData</a></code> (for gene specific
+information) or <code><a href='http://www.rdocumentation.org/packages/Biobase/topics/assayData'>assayData</a></code> (for gene by cell matrices)
+slots. This additional information includes:</p><dl class='dl-horizontal'>
+ <dt><code>phenoData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt>Cell</dt><dd><p>Unique cell identifier.</p></dd>
+ <dt>Group</dt><dd><p>The group or path the cell belongs to.</p></dd>
+ <dt>ExpLibSize</dt><dd><p>The expected library size for that cell.</p></dd>
+ <dt>Step (paths only)</dt><dd><p>how far along the path each cell is.</p></dd>
+ </dl></p></dd>
+ <dt><code>featureData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt>Gene</dt><dd><p>Unique gene identifier.</p></dd>
+ <dt>BaseGeneMean</dt><dd><p>The base expression level for that gene.</p></dd>
+ <dt>OutlierFactor</dt><dd><p>Expression outlier factor for that gene.
+ Values of 1 indicate the gene is not an expression outlier.</p></dd>
+ <dt>GeneMean</dt><dd><p>Expression level after applying outlier factors.</p></dd>
+ <dt>BatchFac[Batch]</dt><dd><p>The batch effects factor for each gene for
+ a particular batch.</p></dd>
+ <dt>DEFac[Group]</dt><dd><p>The differential expression factor for each
+ gene in a particular group. Values of 1 indicate the gene is not
+ differentially expressed.</p></dd>
+ <dt>SigmaFac[Path]</dt><dd><p>Factor applied to genes that have
+ non-linear changes in expression along a path.</p></dd>
+ </dl></p></dd>
+ <dt><code>assayData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt>BatchCellMeans</dt><dd><p>The mean expression of genes in each cell
+ after adding batch effects.</p></dd>
+ <dt>BaseCellMeans</dt><dd><p>The mean expression of genes in each cell
+ after any differential expression and adjusted for expected
+ library size.</p></dd>
+ <dt>BCV</dt><dd><p>The Biological Coefficient of Variation for each gene
+ in each cell.</p></dd>
+ <dt>CellMeans</dt><dd><p>The mean expression level of genes in each cell
+ adjusted for BCV.</p></dd>
+ <dt>TrueCounts</dt><dd><p>The simulated counts before dropout.</p></dd>
+ <dt>Dropout</dt><dd><p>Logical matrix showing which values have been
+ dropped in which cells.</p></dd>
+ </dl></p></dd>
+</dl>
+ <p>Values that have been added by Splatter are named using <code>CamelCase</code> in
+order to differentiate them from the values added by Scater which uses
+<code>underscore_naming</code>.</p>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p><code><a href='splatSimLibSizes.html'>splatSimLibSizes</a></code>, <code><a href='splatSimGeneMeans.html'>splatSimGeneMeans</a></code>,
+<code><a href='splatSimBatchEffects.html'>splatSimBatchEffects</a></code>, <code><a href='splatSimBatchCellMeans.html'>splatSimBatchCellMeans</a></code>,
+<code><a href='splatSimDE.html'>splatSimDE</a></code>, <code><a href='splatSimCellMeans.html'>splatSimCellMeans</a></code>,
+<code><a href='splatSimBCVMeans.html'>splatSimBCVMeans</a></code>, <code><a href='splatSimTrueCounts.html'>splatSimTrueCounts</a></code>,
+<code><a href='splatSimDropout.html'>splatSimDropout</a></code></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'># Simulation with default parameters
+</div><span class='co'># NOT RUN {</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>()
+<span class='co'># Simulation with different number of genes</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>)
+<span class='co'># Simulation with custom parameters</span>
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>mean.rate</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='no'>params</span>)
+<span class='co'># Simulation with adjusted custom parameters</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='no'>params</span>, <span class='kw'>mean.rate</span> <span class='kw'>=</span> <span class='fl'>0.6</span>, <span class='kw'>out.prob</span> <span class='kw'>=</span> <span class='fl'>0.2</span>)
+<span class='co'># Simulate groups</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"groups"</span>)
+<span class='co'># Simulate paths</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"paths"</span>)
+<span class='co'># }</span></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#see-also">See also</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/splatter.html b/docs/reference/splatter.html
new file mode 100644
index 0000000000000000000000000000000000000000..0f14e5d11204c9e2b98c5ec03c7c4c73dc26f2da
--- /dev/null
+++ b/docs/reference/splatter.html
@@ -0,0 +1,135 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>splatter. — splatter • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>splatter.</h1>
+ </div>
+
+
+ <p><span class="pkg">splatter</span> is a package for the well-documented and reproducible
+simulation of single-cell RNA-seq count data.</p>
+
+
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>As well as it's own simulation model <span class="pkg">splatter</span> provides functions for
+the estimation of model parameters.</p>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p>Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA
+Sequencing Data. bioRxiv. 2017; doi:10.1101/133173</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#see-also">See also</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
new file mode 100644
index 0000000000000000000000000000000000000000..4562279c0d13888b8b797ad6f9e4cb70e7593c91
--- /dev/null
+++ b/docs/reference/summariseDiff.html
@@ -0,0 +1,158 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Summarise diffSCESets — summariseDiff • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Summarise diffSCESets</h1>
+ </div>
+
+
+ <p>Summarise the results of <code><a href='diffSCESets.html'>diffSCESets</a></code>. Calculates the Median
+Absolute Deviation (MAD), Mean Absolute Error (MAE) and Root Mean Squared
+Error (RMSE) for the various properties and ranks them.</p>
+
+
+ <pre class="usage"><span class='fu'>summariseDiff</span>(<span class='no'>diff</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>diff</th>
+ <td><p>Output from <code><a href='diffSCESets.html'>diffSCESets</a></code></p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>data.frame with MADs, MAEs, RMSEs, scaled statistics and ranks</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts..</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCESets.html'>diffSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>summary</span> <span class='kw'><-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
+<span class='fu'>head</span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
+#> 1 Splat Mean 2.565952 NaN 1 2.537638 NaN
+#> 2 Splat Variance 11.684223 NaN 1 10.622008 NaN
+#> 3 Splat ZerosGene 35.000000 NaN 1 41.320000 NaN
+#> 4 Splat MeanVar 11.216247 NaN 1 12.248453 NaN
+#> 5 Splat MeanZeros 45.000000 NaN 1 43.040000 NaN
+#> 6 Splat LibSize 60156.000000 NaN 1 62639.300000 NaN
+#> MAERank RMSE RMSEScaled RMSERank
+#> 1 1 3.081167 NaN 1
+#> 2 1 13.288101 NaN 1
+#> 3 1 45.494505 NaN 1
+#> 4 1 15.266613 NaN 1
+#> 5 1 52.700095 NaN 1
+#> 6 1 64195.529851 NaN 1</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/winsorize.html b/docs/reference/winsorize.html
new file mode 100644
index 0000000000000000000000000000000000000000..f6f02b23e73c98a4bb736e2a45e189475f7446f1
--- /dev/null
+++ b/docs/reference/winsorize.html
@@ -0,0 +1,141 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Winsorize vector — winsorize • splatter</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">splatter</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="..//index.html">
+ <span class="fa fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get Started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Winsorize vector</h1>
+ </div>
+
+
+ <p>Set outliers in a numeric vector to a specified percentile.</p>
+
+
+ <pre class="usage"><span class='fu'>winsorize</span>(<span class='no'>x</span>, <span class='no'>q</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>Numeric vector to winsorize</p></td>
+ </tr>
+ <tr>
+ <th>q</th>
+ <td><p>Percentile to set from each end</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Winsorized numeric vector</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>