diff --git a/DESCRIPTION b/DESCRIPTION
index 1fcf06d196f0d20a815654a8e91040afc68dbd72..d05e33eb86f0d7c431ac1e1e08447fe812b3d598 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.5.1
-Date: 2018-06-12
+Version: 1.5.2
+Date: 2018-08-16
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 72b2b25038f118608e2efa25a5ea9d4cce226236..38d1982c0e02ada27f4bccbe3afa98b67ce989bc 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+## Version 1.5.2 (2018-08-16)
+
+* Fix bug in getLNormFactors when reversing factors less than one
+* Update documentation to new Roxygen version (6.1.0)
+* Change varible name in vignette for compatibility with scater
+* Add suggested package checks to tests
+
## Version 1.5.1 (2018-06-12)
* Fix normality testing error in splatEstLib
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 3391060ded73817b152018489dada3c8b6a99edd..093d9c333f315b8eb6231423f8bf8591640b226e 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 3e2fd2138ba497eee311638f451e8d4ed6b24486..50e3705175e21dacff2bcd8234aa72d1c04508b4 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index bf401568135e4083f9b9329d5714d69cac574e91..12847736353c618c8a7f9a0f6219673ca79d496f 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -36,7 +36,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -80,7 +80,7 @@
<h1>Introduction to Splatter</h1>
<h4 class="author">Luke Zappia</h4>
- <h4 class="date">2018-06-12</h4>
+ <h4 class="date">2018-08-16</h4>
<small class="dont-index">Source: <a href="https://github.com/Oshlack/splatter/blob/master/vignettes/splatter.Rmd"><code>vignettes/splatter.Rmd</code></a></small>
<div class="hidden name"><code>splatter.Rmd</code></div>
@@ -110,8 +110,11 @@
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># Load package</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw">library</span>(splatter)</a></code></pre></div>
<pre><code>## Loading required package: SingleCellExperiment</code></pre>
+<pre><code>## Warning: package 'SingleCellExperiment' was built under R version 3.5.1</code></pre>
<pre><code>## Loading required package: SummarizedExperiment</code></pre>
+<pre><code>## Warning: package 'SummarizedExperiment' was built under R version 3.5.1</code></pre>
<pre><code>## Loading required package: GenomicRanges</code></pre>
+<pre><code>## Warning: package 'GenomicRanges' was built under R version 3.5.1</code></pre>
<pre><code>## Loading required package: stats4</code></pre>
<pre><code>## Loading required package: BiocGenerics</code></pre>
<pre><code>## Loading required package: parallel</code></pre>
@@ -136,20 +139,24 @@
## table, tapply, union, unique, unsplit, which, which.max,
## which.min</code></pre>
<pre><code>## Loading required package: S4Vectors</code></pre>
+<pre><code>## Warning: package 'S4Vectors' was built under R version 3.5.1</code></pre>
<pre><code>##
## Attaching package: 'S4Vectors'</code></pre>
<pre><code>## The following object is masked from 'package:base':
##
## expand.grid</code></pre>
<pre><code>## Loading required package: IRanges</code></pre>
+<pre><code>## Warning: package 'IRanges' was built under R version 3.5.1</code></pre>
<pre><code>## Loading required package: GenomeInfoDb</code></pre>
<pre><code>## Loading required package: Biobase</code></pre>
+<pre><code>## Warning: package 'Biobase' was built under R version 3.5.1</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: DelayedArray</code></pre>
+<pre><code>## Warning: package 'DelayedArray' was built under R version 3.5.1</code></pre>
<pre><code>## Loading required package: matrixStats</code></pre>
<pre><code>##
## Attaching package: 'matrixStats'</code></pre>
@@ -157,6 +164,7 @@
##
## anyMissing, rowMedians</code></pre>
<pre><code>## Loading required package: BiocParallel</code></pre>
+<pre><code>## Warning: package 'BiocParallel' was built under R version 3.5.1</code></pre>
<pre><code>##
## Attaching package: 'DelayedArray'</code></pre>
<pre><code>## The following objects are masked from 'package:matrixStats':
@@ -165,17 +173,11 @@
<pre><code>## The following objects are masked from 'package:base':
##
## aperm, apply</code></pre>
-<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1"><span class="co"># Load example data</span></a>
-<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw">library</span>(scater)</a></code></pre></div>
+<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1"><span class="co"># Load example data</span></a>
+<a class="sourceLine" id="cb37-2" data-line-number="2"><span class="kw">library</span>(scater)</a></code></pre></div>
+<pre><code>## Warning: package 'scater' was built under R version 3.5.1</code></pre>
<pre><code>## Loading required package: ggplot2</code></pre>
<pre><code>##
-## Attaching package: 'ggplot2'</code></pre>
-<pre><code>## The following object is masked from 'package:Biobase':
-##
-## exprs</code></pre>
-<pre><code>## Warning: replacing previous import 'ggplot2::exprs' by 'Biobase::exprs'
-## when loading 'scater'</code></pre>
-<pre><code>##
## Attaching package: 'scater'</code></pre>
<pre><code>## The following object is masked from 'package:S4Vectors':
##
@@ -183,18 +185,17 @@
<pre><code>## The following object is masked from 'package:stats':
##
## filter</code></pre>
-<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1"><span class="kw">data</span>(<span class="st">"sc_example_counts"</span>)</a>
-<a class="sourceLine" id="cb37-2" data-line-number="2"><span class="co"># Estimate parameters from example data</span></a>
-<a class="sourceLine" id="cb37-3" data-line-number="3">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
-<pre><code>## NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.</code></pre>
-<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" data-line-number="1"><span class="co"># Simulate data using estimated parameters</span></a>
-<a class="sourceLine" id="cb39-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params)</a></code></pre></div>
+<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1"><span class="kw">data</span>(<span class="st">"sc_example_counts"</span>)</a>
+<a class="sourceLine" id="cb43-2" data-line-number="2"><span class="co"># Estimate parameters from example data</span></a>
+<a class="sourceLine" id="cb43-3" data-line-number="3">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a>
+<a class="sourceLine" id="cb43-4" data-line-number="4"><span class="co"># Simulate data using estimated parameters</span></a>
+<a class="sourceLine" id="cb43-5" data-line-number="5">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params)</a></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 counts...</code></pre>
<pre><code>## Simulating dropout (if needed)...</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>
@@ -329,14 +330,14 @@
<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" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
-<a class="sourceLine" id="cb48-2" data-line-number="2">params</a></code></pre></div>
+<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
+<a class="sourceLine" id="cb52-2" data-line-number="2">params</a></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 498429
+## 10000 100 802677
##
## 28 additional parameters
##
@@ -382,17 +383,17 @@
<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" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></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" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" data-line-number="1">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>)</a>
-<a class="sourceLine" id="cb52-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" data-line-number="1">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>)</a>
+<a class="sourceLine" id="cb56-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></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" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
-<a class="sourceLine" id="cb54-2" data-line-number="2">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>))</a>
-<a class="sourceLine" id="cb54-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
-<a class="sourceLine" id="cb54-4" data-line-number="4"><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>))</a></code></pre></div>
+<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
+<a class="sourceLine" id="cb58-2" data-line-number="2">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>))</a>
+<a class="sourceLine" id="cb58-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
+<a class="sourceLine" id="cb58-4" data-line-number="4"><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>))</a></code></pre></div>
<pre><code>## $nGenes
## [1] 8000
##
@@ -401,15 +402,15 @@
##
## $mean.shape
## [1] 0.6</code></pre>
-<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
-<a class="sourceLine" id="cb56-2" data-line-number="2">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>)</a>
-<a class="sourceLine" id="cb56-3" data-line-number="3">params</a></code></pre></div>
+<div class="sourceCode" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
+<a class="sourceLine" id="cb60-2" data-line-number="2">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>)</a>
+<a class="sourceLine" id="cb60-3" data-line-number="3">params</a></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 498429
+## 8000 100 802677
##
## 28 additional parameters
##
@@ -452,8 +453,8 @@
## 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" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" data-line-number="1">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>)</a>
-<a class="sourceLine" id="cb58-2" data-line-number="2"><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>))</a></code></pre></div>
+<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" data-line-number="1">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>)</a>
+<a class="sourceLine" id="cb62-2" data-line-number="2"><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>))</a></code></pre></div>
<pre><code>## $lib.loc
## [1] 12
##
@@ -465,24 +466,23 @@
<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" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" data-line-number="1"><span class="co"># Check that sc_example counts is an integer matrix</span></a>
-<a class="sourceLine" id="cb60-2" data-line-number="2"><span class="kw">class</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1"><span class="co"># Check that sc_example counts is an integer matrix</span></a>
+<a class="sourceLine" id="cb64-2" data-line-number="2"><span class="kw">class</span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] "matrix"</code></pre>
-<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" data-line-number="1"><span class="kw">typeof</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" data-line-number="1"><span class="kw">typeof</span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] "integer"</code></pre>
-<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span></a>
-<a class="sourceLine" id="cb64-2" data-line-number="2"><span class="kw">dim</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" data-line-number="1"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span></a>
+<a class="sourceLine" id="cb68-2" data-line-number="2"><span class="kw">dim</span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] 2000 40</code></pre>
-<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
-<a class="sourceLine" id="cb66-2" data-line-number="2">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>]</a></code></pre></div>
+<div class="sourceCode" id="cb70"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb70-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
+<a class="sourceLine" id="cb70-2" data-line-number="2">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>]</a></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" id="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
-<pre><code>## NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.</code></pre>
+<div class="sourceCode" id="cb72"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb72-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
<p>Here we estimated parameters from a counts matrix but <code>splatEstimate</code> can also take a <code>SingleCellExperiment</code> object. 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>
@@ -497,16 +497,16 @@
<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" id="cb70"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb70-1" data-line-number="1">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>)</a></code></pre></div>
+<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">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>)</a></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 counts...</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</code></pre>
-<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" data-line-number="1">sim</a></code></pre></div>
+<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" data-line-number="1">sim</a></code></pre></div>
<pre><code>## class: SingleCellExperiment
## dim: 1000 40
## metadata(1): Params
@@ -518,54 +518,57 @@
## reducedDimNames(0):
## spikeNames(0):</code></pre>
<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is <code>SingleCellExperiment</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 a <code>SingleCellExperiment</code> contains phenotype information about each cell (accessed using <code>colData</code>) and feature information about each gene (accessed using <code>rowData</code>). Splatter uses these slots, as well as <code>assays</code>, to store information about the intermediate values of the simulation.</p>
-<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" data-line-number="1"><span class="co"># Access the counts</span></a>
-<a class="sourceLine" id="cb81-2" data-line-number="2"><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>]</a></code></pre></div>
+<div class="sourceCode" id="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" data-line-number="1"><span class="co"># Access the counts</span></a>
+<a class="sourceLine" id="cb84-2" data-line-number="2"><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>]</a></code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0 0 0 0 0
-## Gene2 24 0 15 0 0
-## Gene3 0 112 0 2 0
-## Gene4 0 15 19 8 0
-## Gene5 0 119 0 0 0</code></pre>
-<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" data-line-number="1"><span class="co"># Information about genes</span></a>
-<a class="sourceLine" id="cb83-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+## Gene1 12 0 84 2 0
+## Gene2 166 344 871 3283 1194
+## Gene3 196 0 49 0 0
+## Gene4 0 0 2 0 0
+## Gene5 1806 0 0 0 0</code></pre>
+<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" data-line-number="1"><span class="co"># Information about genes</span></a>
+<a class="sourceLine" id="cb86-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 4 columns
-## Gene BaseGeneMean OutlierFactor GeneMean
-## <factor> <numeric> <numeric> <numeric>
-## 1 Gene1 0.0130414813167312 1 0.0130414813167312
-## 2 Gene2 8.22812161052673 1 8.22812161052673
-## 3 Gene3 94.0106124465794 1 94.0106124465794
-## 4 Gene4 463.408618692168 1 463.408618692168
-## 5 Gene5 8.17204397802014 1 8.17204397802014
-## 6 Gene6 82.8824018477604 1 82.8824018477604</code></pre>
-<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" data-line-number="1"><span class="co"># Information about cells</span></a>
-<a class="sourceLine" id="cb85-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
+## Gene BaseGeneMean OutlierFactor GeneMean
+## <factor> <numeric> <numeric> <numeric>
+## Gene1 Gene1 32.3718444106857 1 32.3718444106857
+## Gene2 Gene2 747.318971058425 1 747.318971058425
+## Gene3 Gene3 326.109389737362 1 326.109389737362
+## Gene4 Gene4 110.418481903485 1 110.418481903485
+## Gene5 Gene5 31.0298971169305 1 31.0298971169305
+## Gene6 Gene6 4.76290936260425 1 4.76290936260425</code></pre>
+<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1"><span class="co"># Information about cells</span></a>
+<a class="sourceLine" id="cb88-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
## Cell Batch ExpLibSize
## <factor> <character> <numeric>
-## Cell1 Cell1 Batch1 417797.914401539
-## Cell2 Cell2 Batch1 292966.340021102
-## Cell3 Cell3 Batch1 29202.3477378194
-## Cell4 Cell4 Batch1 307931.285977102
-## Cell5 Cell5 Batch1 291609.629194382
-## Cell6 Cell6 Batch1 580684.827308051</code></pre>
-<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
-<a class="sourceLine" id="cb87-2" data-line-number="2"><span class="kw">names</span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
+## Cell1 Cell1 Batch1 416832.625556834
+## Cell2 Cell2 Batch1 485547.616871914
+## Cell3 Cell3 Batch1 213084.745731367
+## Cell4 Cell4 Batch1 298739.480020433
+## Cell5 Cell5 Batch1 286377.519263817
+## Cell6 Cell6 Batch1 335445.033244731</code></pre>
+<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
+<a class="sourceLine" id="cb90-2" data-line-number="2"><span class="kw">names</span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
<pre><code>## [1] "BatchCellMeans" "BaseCellMeans" "BCV" "CellMeans"
## [5] "TrueCounts" "counts"</code></pre>
-<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
-<a class="sourceLine" id="cb89-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<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>]</a></code></pre></div>
+<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
+<a class="sourceLine" id="cb92-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<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>]</a></code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 1.770411e-03 2.306051e-27 3.092778e-04 1.730713e-38 3.735798e-35
-## Gene2 2.507370e+01 2.388855e-19 1.629559e+01 1.405443e-05 4.289045e-03
-## Gene3 5.586177e-06 1.059315e+02 1.635766e-07 1.327532e+00 1.695889e-14
-## Gene4 1.129532e+00 1.036317e+01 1.679162e+01 8.609940e+00 5.195456e-11
-## Gene5 3.468714e-02 1.040199e+02 1.169722e-03 1.047193e-01 2.080234e-03</code></pre>
+## Gene1 1.353239e+01 5.985547e-02 81.70412873 4.165728e+00 1.960157e-03
+## Gene2 1.636830e+02 3.550569e+02 885.79020522 3.334211e+03 1.179854e+03
+## Gene3 2.131076e+02 3.205235e-04 52.24270359 3.044254e-05 5.925819e-06
+## Gene4 1.708375e-10 1.486684e-12 1.08476099 2.597789e-08 1.729964e-03
+## Gene5 1.822366e+03 6.290119e-01 0.05023998 7.738061e-03 1.338512e-05</code></pre>
<p>An additional (big) advantage of outputting a <code>SingleCellExperiment</code> is that we get immediate access to other analysis packages, such as the plotting functions in <code>scater</code>. For example we can make a PCA plot:</p>
-<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
-<a class="sourceLine" id="cb91-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim)</a></code></pre></div>
+<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
+<a class="sourceLine" id="cb94-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim)</a></code></pre></div>
+<pre><code>## Warning: 'normalise' is deprecated.
+## Use 'normalize' instead.
+## See help("Deprecated")</code></pre>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
-<a class="sourceLine" id="cb93-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></code></pre></div>
+<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
+<a class="sourceLine" id="cb97-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></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 about the <code>SingleCellExperiment</code> object refer to the [vignette] <a href="https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">SCE-vignette</a>. For information about 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>
@@ -623,11 +626,14 @@
<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" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1">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>,</a>
-<a class="sourceLine" id="cb94-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb94-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<div class="sourceCode" id="cb98"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb98-1" data-line-number="1">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>,</a>
+<a class="sourceLine" id="cb98-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb98-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<pre><code>## Warning: 'normalise' is deprecated.
+## Use 'normalize' instead.
+## See help("Deprecated")</code></pre>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb101"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb101-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></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>
@@ -635,10 +641,13 @@
<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" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1">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>)</a>
-<a class="sourceLine" id="cb97-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
+<div class="sourceCode" id="cb102"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb102-1" data-line-number="1">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>)</a>
+<a class="sourceLine" id="cb102-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
+<pre><code>## Warning: 'normalise' is deprecated.
+## Use 'normalize' instead.
+## See help("Deprecated")</code></pre>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></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>
@@ -646,17 +655,23 @@
<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" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1">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>)</a>
-<a class="sourceLine" id="cb100-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
+<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" data-line-number="1">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>)</a>
+<a class="sourceLine" id="cb106-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
+<pre><code>## Warning: 'normalise' is deprecated.
+## Use 'normalize' instead.
+## See help("Deprecated")</code></pre>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb102"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb102-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></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" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" data-line-number="1">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>),</a>
-<a class="sourceLine" id="cb103-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb103-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<div class="sourceCode" id="cb110"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb110-1" data-line-number="1">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>),</a>
+<a class="sourceLine" id="cb110-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb110-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<pre><code>## Warning: 'normalise' is deprecated.
+## Use 'normalize' instead.
+## See help("Deprecated")</code></pre>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></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>)</a></code></pre></div>
+<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></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>)</a></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>
@@ -670,7 +685,7 @@
<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" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
<pre><code>## Splatter currently contains 13 simulations
##
## Splat (splat)
@@ -725,7 +740,7 @@
## DOI: 10.1093/nar/gkx1113 GitHub: cran/SparseDC
## The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.</code></pre>
<p>(or more conveniently for the vignette as a table)</p>
-<div class="sourceCode" id="cb108"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb108-1" data-line-number="1">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>))</a></code></pre></div>
+<div class="sourceCode" id="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" data-line-number="1">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>))</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">Name</th>
@@ -834,67 +849,60 @@
<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 a <code>SingleCellExperiment</code> object but they require a length for each gene. The <code>addGeneLengths</code> function can be used to simulate these lengths:</p>
-<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" data-line-number="1">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>)</a>
-<a class="sourceLine" id="cb109-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
-<a class="sourceLine" id="cb109-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1">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>)</a>
+<a class="sourceLine" id="cb117-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
+<a class="sourceLine" id="cb117-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
-## Gene GeneMean Length
-## <factor> <numeric> <numeric>
-## 1 Gene1 0.31504131758053 1118
-## 2 Gene2 0.00417585217082588 2098
-## 3 Gene3 0.373634067284232 3416
-## 4 Gene4 0.310092742796264 807
-## 5 Gene5 2.88627905029782 4492
-## 6 Gene6 0.610061028603659 7264</code></pre>
+## Gene GeneMean Length
+## <factor> <numeric> <numeric>
+## Gene1 Gene1 1.63195218364911 3183
+## Gene2 Gene2 2.24908052110884 3558
+## Gene3 Gene3 0.118794797239876 4102
+## Gene4 Gene4 0.582831992501315 612
+## Gene5 Gene5 0.493213594777193 1103
+## Gene6 Gene6 0.881807964448208 1507</code></pre>
<p>We can then use <code>scater</code> to calculate TPM:</p>
-<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
-<a class="sourceLine" id="cb111-2" data-line-number="2"><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>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene2 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene3 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene4 0.09404655 0.00000000 0.00000000 0.00000000 0.09265421
-## Gene5 0.03379144 0.01683821 0.03369681 0.01712314 0.08322790</code></pre>
+<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
+<a class="sourceLine" id="cb119-2" data-line-number="2"><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>]</a></code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 99.11615 148.33343 145.2572 98.70588 147.04199
+## Gene2 0.00000 88.46642 129.9476 132.45398 87.69621
+## Gene3 0.00000 0.00000 0.0000 0.00000 0.00000
+## Gene4 0.00000 514.31950 0.0000 256.68368 254.92083
+## Gene5 143.01301 0.00000 0.0000 0.00000 141.44293</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>compareSCEs</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SingleCellExperiment</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" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" data-line-number="1">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>)</a>
-<a class="sourceLine" id="cb113-2" data-line-number="2">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>)</a>
-<a class="sourceLine" id="cb113-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a></code></pre></div>
-<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.
-## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
-<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" data-line-number="1"><span class="kw">names</span>(comparison)</a></code></pre></div>
+<div class="sourceCode" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" data-line-number="1">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>)</a>
+<a class="sourceLine" id="cb121-2" data-line-number="2">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>)</a>
+<a class="sourceLine" id="cb121-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a>
+<a class="sourceLine" id="cb121-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb121-5" data-line-number="5"><span class="kw">names</span>(comparison)</a></code></pre></div>
<pre><code>## [1] "FeatureData" "PhenoData" "Plots"</code></pre>
-<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
+<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb123-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
<pre><code>## [1] "Means" "Variances" "MeanVar" "LibrarySizes"
## [5] "ZerosGene" "ZerosCell" "MeanZeros"</code></pre>
<p>The returned list has three items. The first two are the combined datasets by gene (<code>FeatureData</code>) and by cell (<code>PhenoData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
-<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb125"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb125-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-means-1.png" width="576" style="display: block; margin: auto;"></p>
<p>These are only a few of the plots you might want to consider but it should be easy to make more using the returned data. For example, we could plot the number of expressed genes against the library size:</p>
-<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
-<a class="sourceLine" id="cb120-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
-<a class="sourceLine" id="cb120-3" data-line-number="3"> <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></a>
-<a class="sourceLine" id="cb120-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb126"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb126-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
+<a class="sourceLine" id="cb126-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
+<a class="sourceLine" id="cb126-3" data-line-number="3"> <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_by_counts, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb126-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>()</a></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>diffSCEs</code> function. Similar to <code>compareSCEs</code> this function takes a list of <code>SingleCellExperiment</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" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</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>)</a></code></pre></div>
-<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.
-## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
-<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb123-1" data-line-number="1">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb127"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb127-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a>
+<a class="sourceLine" id="cb127-2" data-line-number="2">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
<p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
-<div class="sourceCode" id="cb124"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb124-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb128"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb128-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></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">
@@ -902,22 +910,22 @@
<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" id="cb125"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb125-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
-<a class="sourceLine" id="cb125-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
-<a class="sourceLine" id="cb125-3" data-line-number="3">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>)</a>
-<a class="sourceLine" id="cb125-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb125-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
-<a class="sourceLine" id="cb125-6" data-line-number="6">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>)</a>
-<a class="sourceLine" id="cb125-7" data-line-number="7"></a>
-<a class="sourceLine" id="cb125-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
-<a class="sourceLine" id="cb125-9" data-line-number="9">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>)</a></code></pre></div>
+<div class="sourceCode" id="cb129"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb129-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
+<a class="sourceLine" id="cb129-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
+<a class="sourceLine" id="cb129-3" data-line-number="3">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>)</a>
+<a class="sourceLine" id="cb129-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb129-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
+<a class="sourceLine" id="cb129-6" data-line-number="6">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>)</a>
+<a class="sourceLine" id="cb129-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb129-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
+<a class="sourceLine" id="cb129-9" data-line-number="9">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>)</a></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" id="cb126"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb126-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb130"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb130-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
<pre><code>##
## Zappia L, Phipson B, Oshlack A. Splatter: Simulation of
## single-cell RNA sequencing data. Genome Biology. 2017;
@@ -937,7 +945,7 @@
<div id="session-information" class="section level1 unnumbered">
<h1 class="hasAnchor">
<a href="#session-information" class="anchor"></a>Session information</h1>
-<div class="sourceCode" id="cb128"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb128-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
+<div class="sourceCode" id="cb132"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb132-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
<pre><code>## R version 3.5.0 (2018-04-23)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
@@ -954,59 +962,54 @@
## [8] methods base
##
## other attached packages:
-## [1] scater_1.8.0 ggplot2_2.2.1.9000
-## [3] splatter_1.4.0 SingleCellExperiment_1.2.0
-## [5] SummarizedExperiment_1.10.0 DelayedArray_0.6.0
-## [7] BiocParallel_1.14.0 matrixStats_0.53.1
-## [9] Biobase_2.40.0 GenomicRanges_1.32.0
-## [11] GenomeInfoDb_1.16.0 IRanges_2.14.1
-## [13] S4Vectors_0.18.1 BiocGenerics_0.26.0
-## [15] BiocStyle_2.8.0
+## [1] scater_1.9.14 ggplot2_3.0.0.9000
+## [3] splatter_1.5.2 SingleCellExperiment_1.3.10
+## [5] SummarizedExperiment_1.11.6 DelayedArray_0.7.27
+## [7] BiocParallel_1.15.8 matrixStats_0.54.0
+## [9] Biobase_2.41.2 GenomicRanges_1.33.13
+## [11] GenomeInfoDb_1.17.1 IRanges_2.15.16
+## [13] S4Vectors_0.19.19 BiocGenerics_0.27.1
+## [15] BiocStyle_2.9.3
##
## loaded via a namespace (and not attached):
-## [1] bitops_1.0-6 fs_1.2.2
-## [3] rprojroot_1.3-2 tools_3.5.0
-## [5] backports_1.1.2 R6_2.2.2
-## [7] vipor_0.4.5 lazyeval_0.2.1
-## [9] colorspace_1.3-2 sp_1.2-7
-## [11] withr_2.1.2 tidyselect_0.2.4
-## [13] gridExtra_2.3 compiler_3.5.0
-## [15] xml2_1.2.0 desc_1.2.0
-## [17] labeling_0.3 bookdown_0.7
-## [19] scales_0.5.0.9000 checkmate_1.8.6
-## [21] pkgdown_1.1.0 commonmark_1.5
-## [23] stringr_1.3.0 digest_0.6.15
-## [25] rmarkdown_1.9 XVector_0.20.0
-## [27] pkgconfig_2.0.1 htmltools_0.3.6
-## [29] akima_0.6-2 highr_0.6
-## [31] limma_3.36.0 rlang_0.2.0.9001
-## [33] rstudioapi_0.7 shiny_1.0.5
-## [35] DelayedMatrixStats_1.2.0 bindr_0.1.1
-## [37] dplyr_0.7.5 RCurl_1.95-4.10
-## [39] magrittr_1.5 GenomeInfoDbData_1.1.0
-## [41] Matrix_1.2-14 Rcpp_0.12.17
-## [43] ggbeeswarm_0.6.0 munsell_0.4.3
-## [45] Rhdf5lib_1.2.0 viridis_0.5.1
-## [47] stringi_1.2.2 yaml_2.1.19
-## [49] edgeR_3.22.0 MASS_7.3-50
-## [51] zlibbioc_1.26.0 rhdf5_2.24.0
-## [53] plyr_1.8.4 grid_3.5.0
-## [55] promises_1.0.1 shinydashboard_0.7.0
-## [57] crayon_1.3.4 lattice_0.20-35
-## [59] cowplot_0.9.2 splines_3.5.0
-## [61] locfit_1.5-9.1 knitr_1.20
-## [63] pillar_1.2.2 rjson_0.2.15
-## [65] reshape2_1.4.3 glue_1.2.0
-## [67] evaluate_0.10.1 data.table_1.11.0
-## [69] httpuv_1.4.2 gtable_0.2.0
-## [71] purrr_0.2.4 assertthat_0.2.0
-## [73] xfun_0.1 mime_0.5
-## [75] xtable_1.8-2 roxygen2_6.0.1
-## [77] later_0.7.2 survival_2.42-3
-## [79] viridisLite_0.3.0 tibble_1.4.2
-## [81] beeswarm_0.2.3 memoise_1.1.0
-## [83] tximport_1.8.0 bindrcpp_0.2.2
-## [85] fitdistrplus_1.0-9</code></pre>
+## [1] viridis_0.5.1 edgeR_3.23.3
+## [3] splines_3.5.0 viridisLite_0.3.0
+## [5] DelayedMatrixStats_1.3.6 assertthat_0.2.0
+## [7] highr_0.7 sp_1.3-1
+## [9] vipor_0.4.5 GenomeInfoDbData_1.1.0
+## [11] yaml_2.2.0 pillar_1.3.0
+## [13] backports_1.1.2 lattice_0.20-35
+## [15] limma_3.37.3 glue_1.3.0
+## [17] digest_0.6.15 XVector_0.21.3
+## [19] checkmate_1.8.5 colorspace_1.3-2
+## [21] cowplot_0.9.3 htmltools_0.3.6
+## [23] Matrix_1.2-14 plyr_1.8.4
+## [25] pkgconfig_2.0.1 bookdown_0.7
+## [27] zlibbioc_1.27.0 purrr_0.2.5
+## [29] scales_1.0.0 HDF5Array_1.9.9
+## [31] tibble_1.4.2 withr_2.1.2
+## [33] lazyeval_0.2.1 survival_2.42-6
+## [35] magrittr_1.5 crayon_1.3.4
+## [37] memoise_1.1.0 evaluate_0.11
+## [39] fs_1.2.5 MASS_7.3-50
+## [41] xml2_1.2.0 beeswarm_0.2.3
+## [43] fitdistrplus_1.0-9 tools_3.5.0
+## [45] stringr_1.3.1 Rhdf5lib_1.3.1
+## [47] munsell_0.5.0 locfit_1.5-9.1
+## [49] bindrcpp_0.2.2 akima_0.6-2
+## [51] compiler_3.5.0 pkgdown_1.1.0
+## [53] rlang_0.2.1 rhdf5_2.25.4
+## [55] grid_3.5.0 RCurl_1.95-4.11
+## [57] rstudioapi_0.7 labeling_0.3
+## [59] bitops_1.0-6 rmarkdown_1.10
+## [61] gtable_0.2.0 roxygen2_6.1.0
+## [63] reshape2_1.4.3 R6_2.2.2
+## [65] gridExtra_2.3 knitr_1.20
+## [67] dplyr_0.7.6 bindr_0.1.1
+## [69] commonmark_1.5 rprojroot_1.3-2
+## [71] desc_1.2.0 stringi_1.2.4
+## [73] ggbeeswarm_0.6.0 Rcpp_0.12.18
+## [75] tidyselect_0.2.4 xfun_0.3</code></pre>
</div>
</div>
diff --git a/docs/articles/splatter_files/figure-html/batch-groups-1.png b/docs/articles/splatter_files/figure-html/batch-groups-1.png
index e75cd11225e626747dbbc0e3067a7548383d3596..421cf53d9fd8c047220b248c50ad55af3ec65088 100644
Binary files a/docs/articles/splatter_files/figure-html/batch-groups-1.png 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
index bac866462a3915731b05f4df3fd7b39537c880e3..39a4e5fd8875fecc864773c4ecc155331bf093c0 100644
Binary files a/docs/articles/splatter_files/figure-html/batches-1.png 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
index ec00af72b9ba8bbe8fdbfa9e8137f78bcbff45ea..77a5ec43dbe315afc21f7b15f622f70839f01007 100644
Binary files a/docs/articles/splatter_files/figure-html/comparison-libsize-features-1.png 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
index ea455f031f5d7f0445d0df8cdc7a4e97ac2daf2d..20b60de30b45b7003e0a26ae35f93ecd9bb277f6 100644
Binary files a/docs/articles/splatter_files/figure-html/comparison-means-1.png 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
index ef1f18a5bb4512f5a96b7d5ee74a5f7732124067..2d761ba9a537015dbecf4a42a18bd02c65a62023 100644
Binary files a/docs/articles/splatter_files/figure-html/difference-1.png 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
index 0f8519dbf7f105e18a20dfbaa2075856d81a15a8..4baccc21b81c0cd8da1336c11c70a6583fbe6a31 100644
Binary files a/docs/articles/splatter_files/figure-html/difference-qq-1.png 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
index b5e9d9ede072a2516d3f134a84c0efb44d607abd..330487269187af657fd312ae38d03b705bfcac37 100644
Binary files a/docs/articles/splatter_files/figure-html/groups-1.png 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
index d947ac7a194897a7e9483012eff66dc2d87c933e..11f93706e86978366f316e55c535419658890b26 100644
Binary files a/docs/articles/splatter_files/figure-html/paths-1.png 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
index cf357d6020954aec082c5a62bfb3727492e56146..61fe7b3e3c3cf801c22e98cec26e8c2d9c3b9f89 100644
Binary files a/docs/articles/splatter_files/figure-html/pca-1.png and b/docs/articles/splatter_files/figure-html/pca-1.png differ
diff --git a/docs/authors.html b/docs/authors.html
index 131feabd54894741f2917b4e2b6b5ccad3c12fe6..0a0a20428586228b17e5b9e585179adf42e7f683 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/index.html b/docs/index.html
index 653b12d0ccd5d95cc1c51afa326ef578044bafbc..2dbb6234e09d2326320b24f1113356e64814e5fd 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 883f3981a76b0270d1a993349212de7837e96167..a4177e4f70e6ad84bf95dae4b3bc27084a69cc90 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -116,6 +116,16 @@
<small>Source: <a href='https://github.com/Oshlack/splatter/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
+ <div id="version-1-5-2-2018-08-16" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-5-2-2018-08-16" class="anchor"></a>Version 1.5.2 (2018-08-16)</h2>
+<ul>
+<li>Fix bug in getLNormFactors when reversing factors less than one</li>
+<li>Update documentation to new Roxygen version (6.1.0)</li>
+<li>Change varible name in vignette for compatibility with scater</li>
+<li>Add suggested package checks to tests</li>
+</ul>
+</div>
<div id="version-1-5-1-2018-06-12" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-1-2018-06-12" class="anchor"></a>Version 1.5.1 (2018-06-12)</h2>
@@ -603,6 +613,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#version-1-5-2-2018-08-16">1.5.2</a></li>
<li><a href="#version-1-5-1-2018-06-12">1.5.1</a></li>
<li><a href="#version-1-5-0-2018-05-02">1.5.0</a></li>
<li><a href="#version-1-4-1-2018-06-12">1.4.1</a></li>
diff --git a/docs/reference/BASiCSEstimate.html b/docs/reference/BASiCSEstimate.html
index 1969d3dcfcc35f7a8f052ce3d37d800257db863b..91b18889aed276585522a6a2a3889d722b8652db 100644
--- a/docs/reference/BASiCSEstimate.html
+++ b/docs/reference/BASiCSEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -127,8 +127,8 @@
</div>
<pre class="usage"><span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>,
- <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+ <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(),
+ <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='co'># S3 method for SingleCellExperiment</span>
<span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
@@ -136,9 +136,9 @@
<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='co'># S3 method for matrix</span>
-<span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(),
- <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</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">
diff --git a/docs/reference/BASiCSParams.html b/docs/reference/BASiCSParams.html
index ec0bba09ddb6085e4384309e043360c28b35fd97..43e698da9635a3eba3de3ece7b4bdea3b7c7d32d 100644
--- a/docs/reference/BASiCSParams.html
+++ b/docs/reference/BASiCSParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/BASiCSSimulate.html b/docs/reference/BASiCSSimulate.html
index 33befe8843c66bc2de131596dc82d4c402f88dd6..43ca4cf62d8bbd20b5f3d4e77155cd5a1f95ec8d 100644
--- a/docs/reference/BASiCSSimulate.html
+++ b/docs/reference/BASiCSSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/Lun2Params.html b/docs/reference/Lun2Params.html
index 01f8e11d5e74d08012143d6a8fc562dd1ae3df3f..fc08e7de13398241a8e284a391014d7950196d33 100644
--- a/docs/reference/Lun2Params.html
+++ b/docs/reference/Lun2Params.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/LunParams.html b/docs/reference/LunParams.html
index 93e67e423cbb416d9c72a4337433f369f5d43b74..d4d9a5cacb19ff159b51a32ac2cdfc4c78aa1d98 100644
--- a/docs/reference/LunParams.html
+++ b/docs/reference/LunParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/MFAParams.html b/docs/reference/MFAParams.html
index af260c4b6f73fa9f9fb85d53153f7f29f0366519..f452a70f2fbf25644d01956869e8783771ab8c68 100644
--- a/docs/reference/MFAParams.html
+++ b/docs/reference/MFAParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/Params.html b/docs/reference/Params.html
index d7b22ca4ea154ef9d89e9d7af3ab689e40f4729d..e36c2381a0a52be9f15ddc760dd35beb6789cdef 100644
--- a/docs/reference/Params.html
+++ b/docs/reference/Params.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/PhenoParams.html b/docs/reference/PhenoParams.html
index 1e81129040e56ff1bdf7c7a8faff1e6559045577..668f5ad124e8ebddb952688286b483c66b5691a4 100644
--- a/docs/reference/PhenoParams.html
+++ b/docs/reference/PhenoParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/SCDDParams.html b/docs/reference/SCDDParams.html
index df1c87b4b52ba8b340cb03d4775aea021892c9cd..4f1a47f67b89dcbf38e935aa0ed45a0b92217812 100644
--- a/docs/reference/SCDDParams.html
+++ b/docs/reference/SCDDParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/SimpleParams.html b/docs/reference/SimpleParams.html
index cb3d7dc41896b256baa062ec78d110cab92a416c..495628d4369e53d84fa64621ca993458360fe0ca 100644
--- a/docs/reference/SimpleParams.html
+++ b/docs/reference/SimpleParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/SparseDCParams.html b/docs/reference/SparseDCParams.html
index 90bc0db56a720dca8f9d5d82ae106d9c37303f23..1918570376430b644ae5879568020bbbbd65daee 100644
--- a/docs/reference/SparseDCParams.html
+++ b/docs/reference/SparseDCParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/SplatParams.html b/docs/reference/SplatParams.html
index b0799dbd4cdd3141e1c8f995c83c7b69b50fe185..bf45332b6bc9daab4f45dd6df109c0066e4d1074 100644
--- a/docs/reference/SplatParams.html
+++ b/docs/reference/SplatParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/ZINBParams.html b/docs/reference/ZINBParams.html
index e45994ccabb63a9257526d884ce46cb381083c0e..584bdff81001243f988011ea9afe453e3f9ced4c 100644
--- a/docs/reference/ZINBParams.html
+++ b/docs/reference/ZINBParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/addFeatureStats.html b/docs/reference/addFeatureStats.html
index 791c43ee3519df7f6d14c890622242f66d33146c..91cc7cf2974cde861d0c74bf83d1ade84e1d36b2 100644
--- a/docs/reference/addFeatureStats.html
+++ b/docs/reference/addFeatureStats.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -126,8 +126,8 @@
</div>
- <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>
+ <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">
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 84071b50fef533f281205cf0b85df58eb7608bfd..c85af9e3b738bb036022c7ef58876a630bff90f5 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -175,14 +175,14 @@ vector.</p>
<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 dataset...</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'>rowData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> DataFrame with 6 rows and 3 columns
-#> Gene GeneMean Length
-#> <factor> <numeric> <numeric>
-#> 1 Gene1 0.0900534552218277 1226
-#> 2 Gene2 0.522555935307216 1595
-#> 3 Gene3 0.106387591749603 1829
-#> 4 Gene4 0.0338275734283078 1985
-#> 5 Gene5 2.50286626681109 3068
-#> 6 Gene6 0.01126651860221 1939</div><div class='input'># Sample method (human coding genes)
+#> Gene GeneMean Length
+#> <factor> <numeric> <numeric>
+#> Gene1 Gene1 0.00149439660500624 9480
+#> Gene2 Gene2 0.638530797284861 1256
+#> Gene3 Gene3 0.66978667504377 3699
+#> Gene4 Gene4 0.062491626218548 541
+#> Gene5 Gene5 8.35161494115053 2356
+#> Gene6 Gene6 1.73313242191663 3962</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>)
diff --git a/docs/reference/bridge.html b/docs/reference/bridge.html
index d34e6e3ede944b47f705f796e987dbb5f07666b2..96063b836597cb6568f0c3027992d8c48bf3865b 100644
--- a/docs/reference/bridge.html
+++ b/docs/reference/bridge.html
@@ -74,7 +74,7 @@ a random walk with fixed end points." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/compareSCEs.html b/docs/reference/compareSCEs.html
index e713e4171dd249aefa13f084046fcb861499d572..9cf94da3e343e1f21530944d16dac7f7eadb14de 100644
--- a/docs/reference/compareSCEs.html
+++ b/docs/reference/compareSCEs.html
@@ -74,7 +74,7 @@ basic plots comparing them." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -193,9 +193,8 @@ using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplo
<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'>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 dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</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>))</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><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"
+ <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'>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 dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</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">
diff --git a/docs/reference/diffSCEs.html b/docs/reference/diffSCEs.html
index d3169025d7068f32eeed249f20150b1ac308b76f..cdf21036cf762add05f409e04ae9dd6622f72ea2 100644
--- a/docs/reference/diffSCEs.html
+++ b/docs/reference/diffSCEs.html
@@ -74,7 +74,7 @@ basic plots comparing them to a reference." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -215,9 +215,8 @@ using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplo
<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'>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 dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</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>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><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"
+ <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'>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 dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</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">
diff --git a/docs/reference/expandParams.html b/docs/reference/expandParams.html
index edcbbc954b0c63b853ef812f56a4ab86c120620a..17c7f9121b5792350c9280b56aa0ef1bce6c38fd 100644
--- a/docs/reference/expandParams.html
+++ b/docs/reference/expandParams.html
@@ -74,7 +74,7 @@ the number of groups." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/getLNormFactors.html b/docs/reference/getLNormFactors.html
index d6fcd6496772da9b71355070a38b4e2119f43b79..43fb9aed99e35c7625be013eebe6268515731465 100644
--- a/docs/reference/getLNormFactors.html
+++ b/docs/reference/getLNormFactors.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html
index 22ff3ab0771b8f1d03d6b4ad59eb637bc58385e0..0ec6c1a23a20654c2e0f3e2ea431497bd602586c 100644
--- a/docs/reference/getParam.html
+++ b/docs/reference/getParam.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/getParams.html b/docs/reference/getParams.html
index 4916593026b32dba19f70d337922ef0dc921c7d2..73eb7760a6d3897759f546aa59ca36d7bbbf1c11 100644
--- a/docs/reference/getParams.html
+++ b/docs/reference/getParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/getPathOrder.html b/docs/reference/getPathOrder.html
index d31f7fdad4dd20f677abc6aaa689b55e2ecf8980..c595e54a7688029c1e454b72399c92d711d82c32 100644
--- a/docs/reference/getPathOrder.html
+++ b/docs/reference/getPathOrder.html
@@ -74,7 +74,7 @@ already been simulated." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d1b50f2ad20046172f3c2d63ddcef5b4eeb1ea05..6e666954f5135ffd28f6aa1fca3a9940b118bdcb 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index f3c630fe25b3f37657b851ee10715d97388ae05b..fdbc0a450f3b1ef2b30531f844d118ab23c49c4c 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -74,7 +74,7 @@ brief description." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/logistic.html b/docs/reference/logistic.html
index b14362bb5c7583800a1d919d9e44fd43a2af1957..1cc693c9d43ee6faf05e7a04355ea379963069b2 100644
--- a/docs/reference/logistic.html
+++ b/docs/reference/logistic.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/lun2Estimate.html b/docs/reference/lun2Estimate.html
index 2bb05d422084deccf7dfe3e043bd7ec296fc14fb..8b8f48b792a282751853ba55e93a6562b520ce82 100644
--- a/docs/reference/lun2Estimate.html
+++ b/docs/reference/lun2Estimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
index df17cc4a64a659fadbf39315bbf15dae2b93bfda..d4301128a567c40c11fbb9bbd48e959754d2a56b 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -75,7 +75,7 @@ analyses of single-cell RNA-seq data"." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -130,7 +130,8 @@ analyses of single-cell RNA-seq data".</p>
</div>
- <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>
+ <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">
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 4b72cc29a7d2aa44b7f58355a7e4955a5371a1f7..1cfcf58bf8ba94b3fdeffb9fc89e89c09bc65ed8 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -129,7 +129,8 @@
<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 SingleCellExperiment</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='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>
@@ -161,10 +162,7 @@ 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='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)</div><div class='output co'>#> <span class='message'>Loading required package: ggplot2</span></div><div class='output co'>#> <span class='message'></span>
-#> <span class='message'>Attaching package: ‘ggplot2’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:Biobase’:</span>
-#> <span class='message'></span>
-#> <span class='message'> exprs</span></div><div class='output co'>#> <span class='message'></span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)</div><div class='output co'>#> <span class='warning'>Warning: package ‘scater’ was built under R version 3.5.1</span></div><div class='output co'>#> <span class='message'>Loading required package: ggplot2</span></div><div class='output co'>#> <span class='message'></span>
#> <span class='message'>Attaching package: ‘scater’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:S4Vectors’:</span>
#> <span class='message'></span>
#> <span class='message'> rename</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:stats’:</span>
@@ -177,7 +175,7 @@ for more details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 298655
+#> 2000 40 949886
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/lunSimulate.html b/docs/reference/lunSimulate.html
index f3bc17cda36221f9d1385c7f34a5255d27d95519..7c5e2389e21d6fb1ccc7541eac88c00efc1f0036 100644
--- a/docs/reference/lunSimulate.html
+++ b/docs/reference/lunSimulate.html
@@ -75,7 +75,7 @@ sequencing data with many zero counts"." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/makeCompPanel.html b/docs/reference/makeCompPanel.html
index 477caa4c68709cfaa598617f74a207d6b33125b3..443f1fc5fb70087044fdda3f372817729e53c857 100644
--- a/docs/reference/makeCompPanel.html
+++ b/docs/reference/makeCompPanel.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -126,9 +126,9 @@
</div>
- <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>
+ <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">
diff --git a/docs/reference/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
index f1a23a47e03cdc4728be597b4ca1c5a1a5874c74..23bebd77d35698243a3afbcde345883451712e33 100644
--- a/docs/reference/makeDiffPanel.html
+++ b/docs/reference/makeDiffPanel.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -126,9 +126,10 @@
</div>
- <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>
+ <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">
diff --git a/docs/reference/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
index 0447239b7fc2da64024e81cb95fcfad045e5ada5..b327aeca37301368ce34dd3a9f73b8e669fea089 100644
--- a/docs/reference/makeOverallPanel.html
+++ b/docs/reference/makeOverallPanel.html
@@ -74,7 +74,7 @@ single panel." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index a6ada7e46a36bec938d2f9d7f79f4ea42096da4e..226d15ae37cbb9acc06643c801a8b33b695fec33 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -129,7 +129,8 @@
<pre class="usage"><span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())
<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())
+<span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())
<span class='co'># S3 method for matrix</span>
<span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())</pre>
@@ -165,12 +166,13 @@ details on the parameters.</p>
<span class='fu'>library</span>(<span class='no'>scater</span>)
<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>mfaEstimate</span>(<span class='no'>sc_example_counts</span>)</div><div class='output co'>#> <span class='warning'>Warning: replacing previous import ‘ggplot2::exprs’ by ‘Biobase::exprs’ when loading ‘mfa’</span></div><div class='input'><span class='no'>params</span></div><div class='output co'>#> A Params object of class MFAParams
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>mfaEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='no'>params</span></div><div class='output co'>#> A Params object of class MFAParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 298655
+#> 2000 40 949886
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/mfaSimulate.html b/docs/reference/mfaSimulate.html
index 4a81086ba21666caaee3db2d17b28b90defa8926..b7cc0f01ddc3fd60f102bb3c1d81fcedc98e0df4 100644
--- a/docs/reference/mfaSimulate.html
+++ b/docs/reference/mfaSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
index 92379bcbfb030fe5e6d8e0730a2d741a875dc6ba..df87337b751c9f6fa2b1a21c06053b4b6806c997 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -74,7 +74,7 @@ Params subtypes." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index 1982c2684ff9524007f831327721cf9e6b2200b5..aff60c1cdf2314aa98cfd9fa1bb48d37d37e85fa 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -74,7 +74,7 @@ dataset." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -173,7 +173,7 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 298655
+#> 2000 40 949886
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/phenoSimulate.html b/docs/reference/phenoSimulate.html
index d33261144009835ec075c6d40101d26e7036bdce..19d1bd8c37f54b5b2a04ad7a8ec763603b392bf5 100644
--- a/docs/reference/phenoSimulate.html
+++ b/docs/reference/phenoSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/rbindMatched.html b/docs/reference/rbindMatched.html
index 71da9b756b0f43812d1a45da6995ea250757712f..89fc6a4df83252c3753c99ca2d388fbcb5d97b83 100644
--- a/docs/reference/rbindMatched.html
+++ b/docs/reference/rbindMatched.html
@@ -74,7 +74,7 @@ to both." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
index 1a193d98134b172f03811f90ed2941e01aec1ed6..8e34b062c97e119647ef110ee9de652b238beec5 100644
--- a/docs/reference/scDDEstimate.html
+++ b/docs/reference/scDDEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -134,8 +134,9 @@
<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'>conditions</span>, <span class='no'>...</span>)
<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>scDDEstimate</span>(<span class='no'>counts</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='kw'>condition</span> <span class='kw'>=</span> <span class='st'>"condition"</span>, <span class='no'>...</span>)
+<span class='fu'>scDDEstimate</span>(<span class='no'>counts</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='kw'>condition</span> <span class='kw'>=</span> <span class='st'>"condition"</span>, <span class='no'>...</span>)
<span class='co'># S3 method for default</span>
<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(),
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
index 582f002b55f42f1a0bf2e2905f1ff42462e7cd20..64bcf7fb83393483691641624bf42383801a5cc2 100644
--- a/docs/reference/scDDSimulate.html
+++ b/docs/reference/scDDSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -126,8 +126,8 @@
</div>
- <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>
+ <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">
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 0131afc1aa08605c3672c2f27dbb3d47f7f86733..6b02bb8467f7717d8631163bc930b15bb3ff6dcb 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -181,7 +181,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 298655
+#> 100 100 949886
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParamUnchecked.html b/docs/reference/setParamUnchecked.html
index f82ceec7e3fc9e4ed39dc7f1fae6da559e1fb165..4736f3c789e1d7a555e29a7cd9fcbde05055185e 100644
--- a/docs/reference/setParamUnchecked.html
+++ b/docs/reference/setParamUnchecked.html
@@ -74,7 +74,7 @@ VALIDITY!" />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 934c7d4e92aa4b9415aaf2c7340d0ffd6079ac39..affd2925f8e1f28d6220725f2e36b776e0d83633 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -167,7 +167,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (Genes) (Cells) [Seed]
-#> 10000 100 298655
+#> 10000 100 949886
#>
#> 3 additional parameters
#>
@@ -185,7 +185,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 298655
+#> 1000 50 949886
#>
#> 3 additional parameters
#>
@@ -203,7 +203,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 298655
+#> 1000 50 949886
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParamsUnchecked.html b/docs/reference/setParamsUnchecked.html
index e5994b8a0aef14fa79bac60500b63e343cefca88..7e3eecc21379e342f48a084558898d95e2fc83a9 100644
--- a/docs/reference/setParamsUnchecked.html
+++ b/docs/reference/setParamsUnchecked.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/showDFs.html b/docs/reference/showDFs.html
index 147ab81b76b5a25e0b42447160c87aa3e2edbb39..3a5d8892faf8cd86acff68e574108b9968de332b 100644
--- a/docs/reference/showDFs.html
+++ b/docs/reference/showDFs.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/showPP.html b/docs/reference/showPP.html
index 67e6b409547e19902ac8c9d1b4dd821a13e769b0..b4fef4270fdde75885fe414417d6bf2f189497c1 100644
--- a/docs/reference/showPP.html
+++ b/docs/reference/showPP.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/showValues.html b/docs/reference/showValues.html
index 02b16039d0b2dae056876b99757594abc4df0ff4..538282421445eccf641a16b0c4b9b07d31b7a80e 100644
--- a/docs/reference/showValues.html
+++ b/docs/reference/showValues.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 84a811995dad40ec793336a9d4fa314142bdd98c..75fff797f1fa6eb8e9770c6b4850378ecff8342c 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -173,7 +173,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 298655
+#> 2000 40 949886
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/simpleSimulate.html b/docs/reference/simpleSimulate.html
index f4de70e1c0985eafcd3af3ea08818d6c1015f8b5..9d57fc26449b050ed24eb73b392ae369f248f71d 100644
--- a/docs/reference/simpleSimulate.html
+++ b/docs/reference/simpleSimulate.html
@@ -74,7 +74,7 @@ simulated library sizes, differential expression etc." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index 899e59b11c750b3e0ae1731ff87634f618fe91ce..966eda9bb613b76cb9fecc7a7faea134c73610c7 100644
--- a/docs/reference/sparseDCEstimate.html
+++ b/docs/reference/sparseDCEstimate.html
@@ -74,7 +74,7 @@ dataset." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -132,12 +132,12 @@ dataset.</p>
<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())
<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>,
- <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())
+<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>,
+ <span class='no'>nclusters</span>, <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())
<span class='co'># S3 method for matrix</span>
-<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>, <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())</pre>
+<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>,
+ <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -196,7 +196,7 @@ input data. The counts are preprocessed using
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 500 20 298655
+#> 500 20 949886
#>
#> 7 additional parameters
#>
diff --git a/docs/reference/sparseDCSimulate.html b/docs/reference/sparseDCSimulate.html
index 5a82ee919663e209cb459fec68cbd9fb75d3436b..1098190047e698a5de052320a035bf87faf1ab41 100644
--- a/docs/reference/sparseDCSimulate.html
+++ b/docs/reference/sparseDCSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatEstBCV.html b/docs/reference/splatEstBCV.html
index 4ad0eea422ef7bf811b0637a9eb28f72f5ed52db..15609e38363539308e7b9b47e136322aed9955c5 100644
--- a/docs/reference/splatEstBCV.html
+++ b/docs/reference/splatEstBCV.html
@@ -74,7 +74,7 @@ in the edgeR package." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatEstDropout.html b/docs/reference/splatEstDropout.html
index 56a870eeeca2caf6e16bbac73b4466c651be03e8..b9fa5e4a549a8101a81418d3375ecee32fb92996 100644
--- a/docs/reference/splatEstDropout.html
+++ b/docs/reference/splatEstDropout.html
@@ -74,7 +74,7 @@ when simulating dropout." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatEstLib.html b/docs/reference/splatEstLib.html
index 66ef9f54d282dd95a403ee20ce6d3d62f0bb4ccf..26c7d6f1c0ba3f7ab4f662f333067ca8191baafe 100644
--- a/docs/reference/splatEstLib.html
+++ b/docs/reference/splatEstLib.html
@@ -77,7 +77,7 @@ fitdist for details on the fitting." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatEstMean.html b/docs/reference/splatEstMean.html
index b01f37d88492cc23a36342434049167eea8a443a..1e2a33c9dc7a0c9edea0cc33ee9c0a6956797ca9 100644
--- a/docs/reference/splatEstMean.html
+++ b/docs/reference/splatEstMean.html
@@ -74,7 +74,7 @@ simulate gene expression means." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatEstOutlier.html b/docs/reference/splatEstOutlier.html
index 94d41e688d3b5699d5f1af3257afba44699fd21c..be27376cb45d9f0d0db4e14bccb229ca2daa4b36 100644
--- a/docs/reference/splatEstOutlier.html
+++ b/docs/reference/splatEstOutlier.html
@@ -74,7 +74,7 @@ median mean expression level." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index c1e15c9fd5e48bdb19d068bbf29b717ce7ca2dcc..79f6272bbe93e1574f17c955a33f2af4ad840854 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -75,7 +75,7 @@ is done." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -175,7 +175,7 @@ containing count data to estimate parameters from.</p></td>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 298655
+#> 2000 40 949886
#>
#> 28 additional parameters
#>
diff --git a/docs/reference/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
index e65f3519629e3443783541e3b19e9b95a1cb8fb1..c79f7dffdb81c479430a0987d30aa94dee6cce72 100644
--- a/docs/reference/splatSimBCVMeans.html
+++ b/docs/reference/splatSimBCVMeans.html
@@ -75,7 +75,7 @@ and inverse gamma distribution." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
index d64c54efa885e483bdbd753d665cea0047ba553d..ffa0efb11a17d4935cd1eaa5d72bd3bf316e8313 100644
--- a/docs/reference/splatSimBatchCellMeans.html
+++ b/docs/reference/splatSimBatchCellMeans.html
@@ -74,7 +74,7 @@ factors." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
index 688ce6fe57f3e117606c15ef73d5186f4de52c35..1c6cb9eb4a4154906f114d7c4965f01f193042d8 100644
--- a/docs/reference/splatSimBatchEffects.html
+++ b/docs/reference/splatSimBatchEffects.html
@@ -75,7 +75,7 @@ means for each batch." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
index b52081b16275df897292b835b59f86ab3ab1721c..da004c956878b91350c680502f4b131e2f4d36aa 100644
--- a/docs/reference/splatSimCellMeans.html
+++ b/docs/reference/splatSimCellMeans.html
@@ -77,7 +77,7 @@ means are adjusted for each cell's expected library size." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimDE.html b/docs/reference/splatSimDE.html
index d669255f6458feb63dfb33d142f0aef91fd73a71..6dca9008d30962957c7b2034cd7ef3e11ad078e7 100644
--- a/docs/reference/splatSimDE.html
+++ b/docs/reference/splatSimDE.html
@@ -76,7 +76,7 @@ they are simulated in the correct order." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimDropout.html b/docs/reference/splatSimDropout.html
index 5c8756d87f86aed13fb80365b5c34db715a1fb38..e53b1413d804eefd3b31f14e4ba1d9dd8470f87b 100644
--- a/docs/reference/splatSimDropout.html
+++ b/docs/reference/splatSimDropout.html
@@ -76,7 +76,7 @@ to decide which counts should be dropped." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
index aaeb06b4d40808112276e34a8ec7ce457d1a2a8b..dafef605ac9e63d95e7de8855f093ff51ca1c31c 100644
--- a/docs/reference/splatSimGeneMeans.html
+++ b/docs/reference/splatSimGeneMeans.html
@@ -75,7 +75,7 @@ with the median mean expression multiplied by the outlier factor." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
index 09fc70763ca15dc5fe1a8afd5cccddca029c43d7..c625b642250692370e6220af20b68c5f476cca5c 100644
--- a/docs/reference/splatSimLibSizes.html
+++ b/docs/reference/splatSimLibSizes.html
@@ -75,7 +75,7 @@ negative values are set to half the minimum non-zero value." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index 3326a23e106f34a2ac8937ad1888cd15b3255c70..c085c11e9a93fd99c3893406fe75b994844b71bf 100644
--- a/docs/reference/splatSimTrueCounts.html
+++ b/docs/reference/splatSimTrueCounts.html
@@ -75,7 +75,7 @@ group (or path position), expected library size and BCV." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index b9baca42f236d3eb1f3afc9a9733be9d1bc0cc9d..e6db8e53bf0fa5cc80645aa1a3a07d39af06dec1 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -74,7 +74,7 @@ the Splat method." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/splatter.html b/docs/reference/splatter.html
index 0fdb160e89f880d4c1e42d7b7a97fe9526e36835..609e9679f17234bd06e49113227748c8199bf919 100644
--- a/docs/reference/splatter.html
+++ b/docs/reference/splatter.html
@@ -74,7 +74,7 @@ simulation of single-cell RNA-seq count data." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index d5543b478b9a55465985f7446cab7f3f4e171399..02a4caecc667086f0cf60c55dde9c8430d2c7785 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -75,7 +75,7 @@ Error (RMSE) for the various properties and ranks them." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -147,23 +147,22 @@ Error (RMSE) for the various properties and ranks them.</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'>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 dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</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>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><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 2.808554 NaN 1 2.772518 NaN
-#> 2 Splat Variance 11.361681 NaN 1 10.428142 NaN
-#> 3 Splat ZerosGene 40.000000 NaN 1 45.485000 NaN
-#> 4 Splat MeanVar 10.717219 NaN 1 12.528423 NaN
-#> 5 Splat MeanZeros 47.500000 NaN 1 45.605000 NaN
-#> 6 Splat LibSize 50259.000000 NaN 1 55938.050000 NaN
-#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.327546 NaN 1
-#> 2 1 13.298290 NaN 1
-#> 3 1 49.252157 NaN 1
-#> 4 1 15.695765 NaN 1
-#> 5 1 54.819020 NaN 1
-#> 6 1 56998.524432 NaN 1</div></pre>
+ <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'>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 dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</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 2.850369 NaN 1 2.68786 NaN
+#> 2 Splat Variance 10.925370 NaN 1 10.16677 NaN
+#> 3 Splat ZerosGene 35.000000 NaN 1 40.95000 NaN
+#> 4 Splat MeanVar 10.337395 NaN 1 11.82182 NaN
+#> 5 Splat MeanZeros 45.000000 NaN 1 43.48500 NaN
+#> 6 Splat LibSize 63360.000000 NaN 1 63145.30000 NaN
+#> MAERank RMSE RMSEScaled RMSERank
+#> 1 1 3.24744 NaN 1
+#> 2 1 13.01313 NaN 1
+#> 3 1 45.30232 NaN 1
+#> 4 1 15.00130 NaN 1
+#> 5 1 53.57635 NaN 1
+#> 6 1 64157.28039 NaN 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/winsorize.html b/docs/reference/winsorize.html
index 22343e1d320bc085d9444f697b3814c1552385b7..9695afaa8c71aeee5d6d5a2304f645a7cce7774c 100644
--- a/docs/reference/winsorize.html
+++ b/docs/reference/winsorize.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
diff --git a/docs/reference/zinbEstimate.html b/docs/reference/zinbEstimate.html
index 00b5709997ffeacceb89d38812106ae4a1b17aac..1f2d1a77a38b8b61c4c8f4ba922744dc86690fc8 100644
--- a/docs/reference/zinbEstimate.html
+++ b/docs/reference/zinbEstimate.html
@@ -74,7 +74,7 @@ dataset." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>
@@ -129,20 +129,22 @@ dataset.</p>
</div>
<pre class="usage"><span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>, <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>,
- <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</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='no'>...</span>)
-
-<span class='co'># S3 method for SingleCellExperiment</span>
-<span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>, <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>,
+ <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>,
<span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</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='no'>...</span>)
+<span class='co'># S3 method for SingleCellExperiment</span>
+<span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>,
+ <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</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='no'>...</span>)
+
<span class='co'># S3 method for matrix</span>
<span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>, <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>,
- <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</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='no'>...</span>)</pre>
+ <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>,
+ <span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</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='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
diff --git a/docs/reference/zinbSimulate.html b/docs/reference/zinbSimulate.html
index 7ee2636a744b10297d640e15083d701df793abec..b3fa9743cd2e6bab018c1ed932005da98fe313db 100644
--- a/docs/reference/zinbSimulate.html
+++ b/docs/reference/zinbSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.2</span>
</span>
</div>