diff --git a/DESCRIPTION b/DESCRIPTION
index a57545e5fce95b0cf04eae188341fa5d6785ad7a..2bcc42cb68e826fac0b76046f22202878eb598d0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.1.7
-Date: 2017-10-05
+Version: 1.1.8
+Date: 2017-10-13
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 9066d35406e9f8ecbae08b624d504c27a55f56d7..cd02c608bf33df0c29e4eccbbc5c66532e162d64 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+## Version 1.1.8 (2017-10-13)
+
+* Add BASiCS simulation
+* Update Splatter citation
+* Update Lun2 reference
+
## Version 1.1.7 (2017-10-05)
* Add PhenoPath simulation
@@ -209,4 +215,3 @@
* Added splatParams object
* Added functions for interacting with splatParams
-
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 3a8201b24fa0eb72c1e919ca03dd7abcd1891335..0397c06a5453ca4d43d67d852a1cd9949e45d261 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -96,7 +96,7 @@
</header>
<div class="page-header">
- <h1>Articles <small>version 1.1.7</small></h1>
+ <h1>Articles <small>version 1.1.8</small></h1>
</div>
<div class="row">
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index 93aae153288311a4c6e9d4504519e98587ba1ae0..e0d8ac2b787a46c2c758fdce42ee98b38aabb6e8 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -76,7 +76,7 @@
<h1>Introduction to Splatter</h1>
<h4 class="author">Luke Zappia</h4>
- <h4 class="date">2017-10-05</h4>
+ <h4 class="date">2017-10-13</h4>
</div>
@@ -317,7 +317,7 @@ params</code></pre></div>
##
## Global:
## (Genes) (Cells) [Seed]
-## 10000 100 882480
+## 10000 100 237407
##
## 27 additional parameters
##
@@ -390,7 +390,7 @@ params</code></pre></div>
##
## Global:
## (GENES) (Cells) [Seed]
-## 8000 100 882480
+## 8000 100 237407
##
## 27 additional parameters
##
@@ -501,45 +501,45 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Access the counts</span>
<span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0 0 2 0 22
-## Gene2 25024 156 1 24 0
-## Gene3 185 126 2 0 0
-## Gene4 17 0 1 0 0
-## Gene5 0 0 0 0 0</code></pre>
+## Gene1 208 2 0 0 0
+## Gene2 48 0 0 0 0
+## Gene3 0 0 0 240 0
+## Gene4 0 0 12 626 0
+## Gene5 58 0 47 0 0</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about genes</span>
<span class="kw">head</span>(<span class="kw">rowData</span>(sim))</code></pre></div>
<pre><code>## DataFrame with 6 rows and 4 columns
-## Gene BaseGeneMean OutlierFactor GeneMean
-## <factor> <numeric> <numeric> <numeric>
-## 1 Gene1 5.975143e+00 1 5.975143e+00
-## 2 Gene2 6.047020e+02 1 6.047020e+02
-## 3 Gene3 3.407454e+02 1 3.407454e+02
-## 4 Gene4 1.041869e+00 1 1.041869e+00
-## 5 Gene5 6.429022e-03 1 6.429022e-03
-## 6 Gene6 5.051255e+02 1 5.051255e+02</code></pre>
+## Gene BaseGeneMean OutlierFactor GeneMean
+## <factor> <numeric> <numeric> <numeric>
+## 1 Gene1 8.84938916 1 8.84938916
+## 2 Gene2 2.09254274 1 2.09254274
+## 3 Gene3 76.54642638 1 76.54642638
+## 4 Gene4 48.29447650 1 48.29447650
+## 5 Gene5 8.38049805 1 8.38049805
+## 6 Gene6 0.03711706 1 0.03711706</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about cells</span>
<span class="kw">head</span>(<span class="kw">colData</span>(sim))</code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
## Cell Batch ExpLibSize
## <factor> <character> <numeric>
-## Cell1 Cell1 Batch1 413957.7
-## Cell2 Cell2 Batch1 476887.9
-## Cell3 Cell3 Batch1 367310.0
-## Cell4 Cell4 Batch1 147775.6
-## Cell5 Cell5 Batch1 193681.3
-## Cell6 Cell6 Batch1 590802.3</code></pre>
+## Cell1 Cell1 Batch1 369673.5
+## Cell2 Cell2 Batch1 837884.1
+## Cell3 Cell3 Batch1 211900.0
+## Cell4 Cell4 Batch1 469342.1
+## Cell5 Cell5 Batch1 358101.8
+## Cell6 Cell6 Batch1 984061.6</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Gene by cell matrices</span>
<span class="kw">names</span>(<span class="kw">assays</span>(sim))</code></pre></div>
<pre><code>## [1] "BatchCellMeans" "BaseCellMeans" "BCV" "CellMeans"
## [5] "TrueCounts" "counts"</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Example of cell means matrix</span>
<span class="kw">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>]</code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 4.400164e-01 6.304542e-02 1.10406696 8.139464e-10 2.335664e+01
-## Gene2 2.526252e+04 1.595860e+02 0.03470768 2.065810e+01 6.231519e-02
-## Gene3 1.899993e+02 1.229909e+02 1.03528470 4.606624e-03 1.921180e-06
-## Gene4 1.421395e+01 5.383794e-10 0.34678991 7.669389e-03 2.339044e-18
-## Gene5 3.522450e-87 2.621383e-03 0.01039596 3.410733e-82 1.870620e-46</code></pre>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 1.777352e+02 6.087412e-01 6.358857e-17 5.040406e-01 3.086920e-06
+## Gene2 5.735710e+01 8.038331e-06 1.675001e-06 9.275255e-02 5.368496e-08
+## Gene3 1.307104e-03 4.675363e-09 7.657201e-20 2.453874e+02 1.578852e+00
+## Gene4 2.107991e-04 1.060652e-03 1.201788e+01 6.365346e+02 5.394848e-17
+## Gene5 6.441256e+01 8.666657e-05 4.797971e+01 9.699099e-08 8.152520e-15</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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plotPCA</span>(sim, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
<p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
@@ -640,7 +640,7 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
<a href="#other-simulations" class="anchor"></a>Other simulations</h1>
<p>As well as it’s own Splat simulation method the Splatter package contains implementations of other single-cell RNA-seq simulations that have been published or wrappers around simulations included in other packages. To see all the available simulations run the <code><a href="../reference/listSims.html">listSims()</a></code> function:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</code></pre></div>
-<pre><code>## Splatter currently contains 9 simulations
+<pre><code>## Splatter currently contains 11 simulations
##
## Splat (splat)
## DOI: GitHub:
@@ -676,7 +676,15 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
##
## mfa (mfa)
## DOI: 10.12688/wellcomeopenres.11087.1 GitHub: kieranrcampbell/mfa
-## The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.</code></pre>
+## The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.
+##
+## PhenoPath (pheno)
+## DOI: 10.1101/159913 GitHub: kieranrcampbell/phenopath
+## The PhenoPath simulation produces a pseudotime trajectory with different types of genes.
+##
+## ZINB-WaVE (zinb)
+## DOI: 10.1101/125112 GitHub: drisso/zinbwave
+## The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.</code></pre>
<p>(or more conveniently for the vignette as a table)</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</code></pre></div>
<table class="table">
@@ -751,6 +759,20 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
<td align="left">kieranrcampbell/mfa</td>
<td align="left">The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.</td>
</tr>
+<tr class="even">
+<td align="left">PhenoPath</td>
+<td align="left">pheno</td>
+<td align="left">10.1101/159913</td>
+<td align="left">kieranrcampbell/phenopath</td>
+<td align="left">The PhenoPath simulation produces a pseudotime trajectory with different types of genes.</td>
+</tr>
+<tr class="odd">
+<td align="left">ZINB-WaVE</td>
+<td align="left">zinb</td>
+<td align="left">10.1101/125112</td>
+<td align="left">drisso/zinbwave</td>
+<td align="left">The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.</td>
+</tr>
</tbody>
</table>
<p>Each simulation has it’s own prefix which gives the name of the functions associated with that simulation. For example the prefix for the simple simulation is <code>simple</code> so it would store it’s parameters in a <code>SimpleParams</code> object that can be created using <code><a href="../reference/newParams.html">newSimpleParams()</a></code> or estimated from real data using <code><a href="../reference/simpleEstimate.html">simpleEstimate()</a></code>. To simulate data using that simulation you would use <code><a href="../reference/simpleSimulate.html">simpleSimulate()</a></code>. Each simulation returns a <code>SingleCellExperiment</code> object with intermediate values similar to that returned by <code><a href="../reference/splatSimulate.html">splatSimulate()</a></code>. For more detailed information on each simulation see the appropriate help page (eg. <code><a href="../reference/simpleSimulate.html">?simpleSimulate</a></code> for information on how the simple simulation works or <code><a href="../reference/lun2Estimate.html">? lun2Estimate</a></code> for details of how the Lun 2 simulation estimates parameters) or refer to the appropriate paper or package.</p>
@@ -765,21 +787,21 @@ sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGene
<pre><code>## DataFrame with 6 rows and 3 columns
## Gene GeneMean Length
## <factor> <numeric> <numeric>
-## 1 Gene1 1.60506942 1775
-## 2 Gene2 2.17500094 4361
-## 3 Gene3 1.16851643 2915
-## 4 Gene4 0.01040965 16794
-## 5 Gene5 0.06781127 948
-## 6 Gene6 3.03114500 3089</code></pre>
+## 1 Gene1 0.11512934 9592
+## 2 Gene2 1.08395798 1260
+## 3 Gene3 0.07297126 7150
+## 4 Gene4 0.52861074 2131
+## 5 Gene5 2.07154719 1787
+## 6 Gene6 1.48581784 885</code></pre>
<p>We can then use <code>scater</code> to calculate TPM:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw">calculateTPM</span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)
<span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0.08215535 0.04069785 0.08360619 0.08404271 0.08403017
-## Gene2 0.03343860 0.01656470 0.13611647 0.00000000 0.06840337
-## Gene3 0.00000000 0.02478171 0.05090943 0.02558762 0.02558380
-## Gene4 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene5 0.00000000 0.07620114 0.00000000 0.00000000 0.00000000</code></pre>
+## Gene1 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
+## Gene2 0.06020259 0.00000000 0.05823678 0.00000000 0.11723920
+## Gene3 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
+## Gene4 0.00000000 0.03420037 0.00000000 0.00000000 0.00000000
+## Gene5 0.12734516 0.16313595 0.08212461 0.08100124 0.08266446</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">
@@ -856,7 +878,7 @@ cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumenta
<h1 class="hasAnchor">
<a href="#session-information" class="anchor"></a>Session information</h1>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">sessionInfo</span>()</code></pre></div>
-<pre><code>## R version 3.4.1 (2017-06-30)
+<pre><code>## R version 3.4.2 (2017-09-28)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
@@ -872,54 +894,61 @@ cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumenta
## [8] methods base
##
## other attached packages:
-## [1] splatter_1.1.6 scater_1.5.16
+## [1] splatter_1.1.7 scater_1.5.16
## [3] SingleCellExperiment_0.99.4 SummarizedExperiment_1.7.10
## [5] DelayedArray_0.3.21 matrixStats_0.52.2
-## [7] GenomicRanges_1.29.14 GenomeInfoDb_1.13.4
-## [9] IRanges_2.11.17 S4Vectors_0.15.10
-## [11] ggplot2_2.2.1.9000 Biobase_2.37.2
-## [13] BiocGenerics_0.23.2
+## [7] GenomicRanges_1.29.15 GenomeInfoDb_1.13.5
+## [9] IRanges_2.11.19 S4Vectors_0.15.12
+## [11] ggplot2_2.2.1 Biobase_2.37.2
+## [13] BiocGenerics_0.23.3
##
## loaded via a namespace (and not attached):
-## [1] viridis_0.4.0 edgeR_3.19.6
-## [3] splines_3.4.1 bit64_0.9-7
-## [5] viridisLite_0.2.0 shiny_1.0.5
-## [7] assertthat_0.2.0 highr_0.6
-## [9] sp_1.2-5 blob_1.1.0
-## [11] GenomeInfoDbData_0.99.1 vipor_0.4.5
-## [13] yaml_2.1.14 progress_1.1.2
-## [15] RSQLite_2.0 backports_1.1.1
-## [17] lattice_0.20-35 glue_1.1.1
-## [19] limma_3.33.12 digest_0.6.12
-## [21] checkmate_1.8.4 XVector_0.17.1
-## [23] colorspace_1.3-2 cowplot_0.8.0
-## [25] htmltools_0.3.6 httpuv_1.3.5
-## [27] Matrix_1.2-11 plyr_1.8.4
-## [29] XML_3.98-1.9 pkgconfig_2.0.1
-## [31] biomaRt_2.33.4 zlibbioc_1.23.0
-## [33] xtable_1.8-2 scales_0.5.0.9000
-## [35] BiocParallel_1.11.9 tibble_1.3.4
-## [37] lazyeval_0.2.0 survival_2.41-3
-## [39] magrittr_1.5 mime_0.5
-## [41] memoise_1.1.0 evaluate_0.10.1
-## [43] MASS_7.3-47 beeswarm_0.2.3
-## [45] shinydashboard_0.6.1 fitdistrplus_1.0-9
-## [47] tools_3.4.1 data.table_1.10.4
-## [49] prettyunits_1.0.2 stringr_1.2.0
-## [51] munsell_0.4.3 locfit_1.5-9.1
-## [53] AnnotationDbi_1.39.3 bindrcpp_0.2
-## [55] akima_0.6-2 compiler_3.4.1
-## [57] rlang_0.1.2 rhdf5_2.21.6
-## [59] grid_3.4.1 RCurl_1.95-4.8
-## [61] tximport_1.5.0 rjson_0.2.15
-## [63] labeling_0.3 bitops_1.0-6
-## [65] rmarkdown_1.6 gtable_0.2.0
-## [67] DBI_0.7 reshape2_1.4.2
-## [69] R6_2.2.2 gridExtra_2.3
-## [71] knitr_1.17 dplyr_0.7.4
-## [73] bit_1.1-12 bindr_0.1
-## [75] rprojroot_1.2 stringi_1.1.5
-## [77] ggbeeswarm_0.6.0 Rcpp_0.12.13</code></pre>
+## [1] bitops_1.0-6 bit64_0.9-7
+## [3] progress_1.1.2 rprojroot_1.2
+## [5] zinbwave_0.99.9 numDeriv_2016.8-1
+## [7] tools_3.4.2 backports_1.1.1
+## [9] R6_2.2.2 vipor_0.4.5
+## [11] DBI_0.7 lazyeval_0.2.0
+## [13] colorspace_1.3-2 sp_1.2-5
+## [15] gridExtra_2.3 prettyunits_1.0.2
+## [17] bit_1.1-12 compiler_3.4.2
+## [19] glmnet_2.0-13 pspline_1.0-18
+## [21] labeling_0.3 scales_0.5.0
+## [23] checkmate_1.8.4 mvtnorm_1.0-6
+## [25] stringr_1.2.0 digest_0.6.12
+## [27] rmarkdown_1.6 XVector_0.17.1
+## [29] pkgconfig_2.0.1 htmltools_0.3.6
+## [31] akima_0.6-2 highr_0.6
+## [33] stabledist_0.7-1 ADGofTest_0.3
+## [35] limma_3.33.14 rlang_0.1.2.9000
+## [37] RSQLite_2.0 shiny_1.0.5
+## [39] bindr_0.1 BiocParallel_1.11.11
+## [41] dplyr_0.7.4 RCurl_1.95-4.8
+## [43] magrittr_1.5 GenomeInfoDbData_0.99.1
+## [45] Matrix_1.2-11 Rcpp_0.12.13
+## [47] ggbeeswarm_0.6.0 munsell_0.4.3
+## [49] viridis_0.4.0 stringi_1.1.5
+## [51] yaml_2.1.14 edgeR_3.19.7
+## [53] MASS_7.3-47 zlibbioc_1.23.0
+## [55] rhdf5_2.21.6 plyr_1.8.4
+## [57] grid_3.4.2 blob_1.1.0
+## [59] shinydashboard_0.6.1 lattice_0.20-35
+## [61] cowplot_0.8.0 splines_3.4.2
+## [63] locfit_1.5-9.1 knitr_1.17
+## [65] rjson_0.2.15 softImpute_1.4
+## [67] codetools_0.2-15 reshape2_1.4.2
+## [69] biomaRt_2.33.4 XML_3.98-1.9
+## [71] glue_1.1.1 evaluate_0.10.1
+## [73] data.table_1.10.4-2 httpuv_1.3.5
+## [75] foreach_1.4.3 gtable_0.2.0
+## [77] assertthat_0.2.0 mime_0.5
+## [79] xtable_1.8-2 survival_2.41-3
+## [81] pcaPP_1.9-72 viridisLite_0.2.0
+## [83] gsl_1.9-10.3 tibble_1.3.4
+## [85] copula_0.999-18 iterators_1.0.8
+## [87] AnnotationDbi_1.39.4 beeswarm_0.2.3
+## [89] memoise_1.1.0 tximport_1.5.1
+## [91] bindrcpp_0.2 fitdistrplus_1.0-9</code></pre>
</div>
</div>
</div>
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diff --git a/docs/authors.html b/docs/authors.html
index 8b6f31e5539fc3f34e565d02650db0182ad651a6..52fbe4076f3918a4d4da00ca7aa5af3e47dd9159 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -103,17 +103,17 @@
</div>
<p>Zappia L, Phipson B and Oshlack A (2017).
-“Splatter: Simulation Of Single-Cell RNA Sequencing Data.”
-<em>bioRxiv</em>.
-doi: <a href="http://doi.org/10.1101/133173">10.1101/133173</a>, <a href="http://dx.doi.org/10.1101/133173">http://dx.doi.org/10.1101/133173</a>.
+“Splatter: simulation of single-cell RNA sequencing data.”
+<em>Genome Biology</em>.
+doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-0</a>, <a href="http://dx.doi.org/10.1186/s13059-017-1305-0">http://dx.doi.org/10.1186/s13059-017-1305-0</a>.
</p>
<pre>@Article{,
author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
- title = {Splatter: Simulation Of Single-Cell RNA Sequencing Data},
- journal = {bioRxiv},
+ title = {Splatter: simulation of single-cell RNA sequencing data},
+ journal = {Genome Biology},
year = {2017},
- url = {http://dx.doi.org/10.1101/133173},
- doi = {10.1101/133173},
+ url = {http://dx.doi.org/10.1186/s13059-017-1305-0},
+ doi = {10.1186/s13059-017-1305-0},
}</pre>
<div class="page-header">
<h1>Authors</h1>
diff --git a/docs/news/index.html b/docs/news/index.html
index a33131ead1bdf1d58d7987e3f3ff5774a253791d..71c2603f53a2ef7fe5e51a7df7e83990cc71029b 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -103,6 +103,15 @@
</div>
<div class="contents">
+ <div id="version-1-1-8-2017-10-13" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-1-8-2017-10-13" class="anchor"></a>Version 1.1.8 (2017-10-13)</h2>
+<ul>
+<li>Add BASiCS simulation</li>
+<li>Update Splatter citation</li>
+<li>Update Lun2 reference</li>
+</ul>
+</div>
<div id="version-1-1-7-2017-10-05" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-1-7-2017-10-05" class="anchor"></a>Version 1.1.7 (2017-10-05)</h2>
@@ -448,6 +457,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#version-1-1-8-2017-10-13">1.1.8</a></li>
<li><a href="#version-1-1-7-2017-10-05">1.1.7</a></li>
<li><a href="#version-1-1-6-2017-10-02">1.1.6</a></li>
<li><a href="#version-1-1-5-2017-09-13">1.1.5</a></li>
diff --git a/docs/reference/BASiCSEstimate.html b/docs/reference/BASiCSEstimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..ba67f96f9a1acf5b2153caee7614daf0a6514a91
--- /dev/null
+++ b/docs/reference/BASiCSEstimate.html
@@ -0,0 +1,226 @@
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate BASiCS simulation parameters</h1>
+ </div>
+
+
+ <p>Estimate simulation parameters for the BASiCS simulation from a real dataset.</p>
+
+
+ <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='co'># S3 method for SCESet</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>)
+
+<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>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>either a counts matrix or an SCESet object containing count
+data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>spike.info</th>
+ <td><p>data.frame describing spike-ins with two columns: "Name"
+giving the names of the spike-in features (must match
+<code>rownames(counts)</code>) and "Input" giving the number of input
+molecules.</p></td>
+ </tr>
+ <tr>
+ <th>batch</th>
+ <td><p>vector giving the batch that each cell belongs to.</p></td>
+ </tr>
+ <tr>
+ <th>n</th>
+ <td><p>total number of MCMC iterations. Must be <code>>= max(4, thin)</code> and
+a multiple of <code>thin</code>.</p></td>
+ </tr>
+ <tr>
+ <th>thin</th>
+ <td><p>thining period for the MCMC sampler. Must be <code>>= 2</code>.</p></td>
+ </tr>
+ <tr>
+ <th>burn</th>
+ <td><p>burn-in period for the MCMC sampler. Must be in the range
+<code>1 <= burn < n</code> and a multiple of <code>thin</code>.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>BASiCSParams object to store estimated values in.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages.</p></td>
+ </tr>
+ <tr>
+ <th>progress</th>
+ <td><p>logical. Whether to print additional BASiCS progress
+messages.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Optional parameters passed to <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>BASiCSParams object containing the estimated parameters.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> that
+takes the output and converts it to a BASiCSParams object. Either a set of
+spike-ins or batch information (or both) must be supplied. If only batch
+information is provided there must be at least two batches. See
+<code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> for details.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='no'>spike.info</span> <span class='kw'><-</span> <span class='fu'>data.frame</span>(<span class='kw'>Name</span> <span class='kw'>=</span> <span class='fu'>rownames</span>(<span class='no'>sc_example_counts</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>],
+ <span class='kw'>Input</span> <span class='kw'>=</span> <span class='fu'>rnorm</span>(<span class='fl'>10</span>, <span class='fl'>500</span>, <span class='fl'>200</span>),
+ <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>BASiCSEstimate</span>(<span class='no'>sc_example_counts</span>[<span class='fl'>1</span>:<span class='fl'>50</span>, <span class='fl'>1</span>:<span class='fl'>20</span>],
+ <span class='no'>spike.info</span>)
+<span class='no'>params</span>
+<span class='co'># }</span></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
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+
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+</html>
diff --git a/docs/reference/BASiCSParams.html b/docs/reference/BASiCSParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..b15e37bd6414e05eea5cd4ba74d0497c2c1040bc
--- /dev/null
+++ b/docs/reference/BASiCSParams.html
@@ -0,0 +1,170 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+</li>
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+</li>
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+</li>
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+
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+
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+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The BASiCSParams class</h1>
+ </div>
+
+
+ <p>S4 class that holds parameters for the BASiCS simulation.</p>
+
+
+
+ <h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
+
+
+ <p>The BASiCS simulation uses the following parameters:</p><dl class='dl-horizontal'>
+ <dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
+ <dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
+ <dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+ <dt><em>Batch parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>nBatches</code></dt><dd><p>Number of batches to simulate.</p></dd>
+ <dt><code>batchCells</code></dt><dd><p>Number of cells in each batch.</p></dd>
+ </dl></p></dd>
+ <dt><em>Gene parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>gene.params</code></dt><dd><p>A <code>data.frame</code> containing gene
+ parameters with two coloumns: <code>Mean</code> (mean expression for
+ each biological gene) and <code>Delta</code> (cell-to-cell
+ heterogeneity for each biological gene).</p></dd>
+ </dl></p></dd>
+ <dt><em>Spike-in parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>nSpikes</code></dt><dd><p>The number of spike-ins to simulate.</p></dd>
+ <dt><code>spike.means</code></dt><dd><p>Input molecules for each spike-in.</p></dd>
+ </dl></p></dd>
+ <dt><em>Cell parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>cell.params</code></dt><dd><p>A <code>data.frame</code> containing gene
+ parameters with two coloumns: <code>Phi</code> (mRNA content factor for
+ each cell, scaled to sum to the number of cells in each batch)
+ and <code>S</code> (capture efficient for each cell).</p></dd>
+ </dl></p></dd>
+ <dt><em>Variability parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>theta</code></dt><dd><p>Technical variability parameter for each
+ batch.</p></dd>
+ </dl></p></dd>
+</dl>
+ <p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='BASiCSEstimate.html'>BASiCSEstimate</a></code>. For details of the BASiCS simulation see
+<code><a href='BASiCSSimulate.html'>BASiCSSimulate</a></code>.</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
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diff --git a/docs/reference/BASiCSSimulate.html b/docs/reference/BASiCSSimulate.html
new file mode 100644
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+++ b/docs/reference/BASiCSSimulate.html
@@ -0,0 +1,181 @@
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>BASiCS simulation</h1>
+ </div>
+
+
+ <p>Simulate counts using the BASiCS method.</p>
+
+
+ <pre class="usage"><span class='fu'>BASiCSSimulate</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='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>BASiCSParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment containing simulated counts</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> that
+takes a <code><a href='BASiCSParams.html'>BASiCSParams</a></code>, runs the simulation then converts the
+output to an <code><a href='http://www.rdocumentation.org/packages/scater/topics/SCESet'>SCESet</a></code> object. See
+<code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> for more details of how the simulation
+works.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of
+Single-Cell Sequencing data. PLoS Comput. Biol. (2015).</p>
+<p>Paper: <a href='10.1371/journal.pcbi.1004333'>10.1371/journal.pcbi.1004333</a></p>
+<p>Code: <a href='https://github.com/catavallejos/BASiCS'>https://github.com/catavallejos/BASiCS</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>BASiCSSimulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='warning'>Warning: Number of gene.params not equal to nGenes, gene.params will be sampled.</span></div><div class='output co'>#> <span class='warning'>Warning: Number of cell.params not equal to nCells, cell.params will be sampled.</span></div><div class='output co'>#> <span class='message'>Simulating counts with BASiCS...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='output co'>#> <span class='message'>Done!</span></div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/Lun2Params.html b/docs/reference/Lun2Params.html
index f98a23ca3f03d74fc492ff120f9fba6b2ca7c311..6d912230a51cc362914aecb3e01db0e38b0fcb58 100644
--- a/docs/reference/Lun2Params.html
+++ b/docs/reference/Lun2Params.html
@@ -102,7 +102,7 @@
</div>
- <p>S4 class that holds parameters for the Lun simulation.</p>
+ <p>S4 class that holds parameters for the Lun2 simulation.</p>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 9fa10ffe6a1724705b175161d6e785c1e0715034..b6a9822baabea89b856596969d345db80946c8df 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -154,14 +154,14 @@ 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 0.8455684 1284
-#> 2 Gene2 0.1606091 5127
-#> 3 Gene3 6.7083234 1847
-#> 4 Gene4 0.2917321 2194
-#> 5 Gene5 1.4748643 1567
-#> 6 Gene6 0.0326816 7629</div><div class='input'># Sample method (human coding genes)
+#> Gene GeneMean Length
+#> <factor> <numeric> <numeric>
+#> 1 Gene1 0.7546303813 885
+#> 2 Gene2 0.1242896647 2280
+#> 3 Gene3 0.1160044662 3160
+#> 4 Gene4 0.1938835897 1612
+#> 5 Gene5 0.0020382615 1890
+#> 6 Gene6 0.0006305612 1488</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/expandParams.html b/docs/reference/expandParams.html
index f0013003ed880ff2a2a4868bf13867f469ccee2a..9b7b0e3d2d7fb0c6727155bf415eff3d49b9c435 100644
--- a/docs/reference/expandParams.html
+++ b/docs/reference/expandParams.html
@@ -108,6 +108,9 @@ the number of groups.</p>
<pre class="usage"><span class='fu'>expandParams</span>(<span class='no'>object</span>, <span class='no'>...</span>)
+<span class='co'># S4 method for BASiCSParams</span>
+<span class='fu'>expandParams</span>(<span class='no'>object</span>)
+
<span class='co'># S4 method for LunParams</span>
<span class='fu'>expandParams</span>(<span class='no'>object</span>)
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 3697b90316d31166e41d778508a961047ef7f515..5cb5e3398c3b1b55529090eb278472970ab326af 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -100,7 +100,7 @@
<div class="page-header">
<h1>
Reference
- <small>version 1.1.7</small>
+ <small>version 1.1.8</small>
</h1>
</div>
@@ -120,6 +120,12 @@
</th>
</tr>
<tr>
+ <!-- -->
+ <td>
+ <p><code><a href="newParams.html">newBASiCSParams</a></code> <code><a href="newParams.html">newLun2Params</a></code> <code><a href="newParams.html">newLunParams</a></code> <code><a href="newParams.html">newMFAParams</a></code> <code><a href="newParams.html">newPhenoParams</a></code> <code><a href="newParams.html">newSCDDParams</a></code> <code><a href="newParams.html">newSimpleParams</a></code> <code><a href="newParams.html">newSplatParams</a></code> <code><a href="newParams.html">newZINBParams</a></code> </p>
+ </td>
+ <td><p>New Params</p></td>
+ </tr><tr>
<!-- -->
<td>
<p><code><a href="getParam.html">getParam</a></code> </p>
@@ -134,73 +140,73 @@
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="setParam.html">setParam</a></code> </p>
</td>
- <td><p>The Lun2Params class</p></td>
+ <td><p>Set a parameter</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="setParams.html">setParams</a></code> </p>
</td>
- <td><p>The LunParams class</p></td>
+ <td><p>Set parameters</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="BASiCSParams.html">BASiCSParams</a></code> </p>
</td>
- <td><p>The MFAParams class</p></td>
+ <td><p>The BASiCSParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="newParams.html">newLun2Params</a></code> <code><a href="newParams.html">newLunParams</a></code> <code><a href="newParams.html">newMFAParams</a></code> <code><a href="newParams.html">newPhenoParams</a></code> <code><a href="newParams.html">newSCDDParams</a></code> <code><a href="newParams.html">newSimpleParams</a></code> <code><a href="newParams.html">newSplatParams</a></code> <code><a href="newParams.html">newZINBParams</a></code> </p>
+ <p><code><a href="Lun2Params.html">Lun2Params</a></code> </p>
</td>
- <td><p>New Params</p></td>
+ <td><p>The Lun2Params class</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="LunParams.html">LunParams</a></code> </p>
</td>
- <td><p>The Params virtual class</p></td>
+ <td><p>The LunParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="MFAParams.html">MFAParams</a></code> </p>
</td>
- <td><p>The PhenoParams class</p></td>
+ <td><p>The MFAParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="Params.html">Params</a></code> </p>
</td>
- <td><p>The SCDDParams class</p></td>
+ <td><p>The Params virtual class</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="PhenoParams.html">PhenoParams</a></code> </p>
</td>
- <td><p>The SimpleParams class</p></td>
+ <td><p>The PhenoParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="SCDDParams.html">SCDDParams</a></code> </p>
</td>
- <td><p>The SplatParams class</p></td>
+ <td><p>The SCDDParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="setParam.html">setParam</a></code> </p>
+ <p><code><a href="SimpleParams.html">SimpleParams</a></code> </p>
</td>
- <td><p>Set a parameter</p></td>
+ <td><p>The SimpleParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p><code><a href="setParams.html">setParams</a></code> </p>
+ <p><code><a href="SplatParams.html">SplatParams</a></code> </p>
</td>
- <td><p>Set parameters</p></td>
+ <td><p>The SplatParams class</p></td>
</tr><tr>
<!-- -->
<td>
- <p></p>
+ <p><code><a href="ZINBParams.html">ZINBParams</a></code> </p>
</td>
<td><p>The ZINBParams class</p></td>
</tr>
@@ -212,6 +218,12 @@
</th>
</tr>
<tr>
+ <!-- -->
+ <td>
+ <p><code><a href="BASiCSEstimate.html">BASiCSEstimate</a></code> </p>
+ </td>
+ <td><p>Estimate BASiCS simulation parameters</p></td>
+ </tr><tr>
<!-- -->
<td>
<p><code><a href="lun2Estimate.html">lun2Estimate</a></code> </p>
@@ -298,6 +310,12 @@
</th>
</tr>
<tr>
+ <!-- -->
+ <td>
+ <p><code><a href="BASiCSSimulate.html">BASiCSSimulate</a></code> </p>
+ </td>
+ <td><p>BASiCS simulation</p></td>
+ </tr><tr>
<!-- -->
<td>
<p><code><a href="lun2Simulate.html">lun2Simulate</a></code> </p>
diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index dca08b58960dfd1925bdb25b7db37f28e96a8060..2393fa095adb1e6eaa7eae4f68698a8810abf187 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -124,26 +124,26 @@ displayed.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>listSims</span>()</div><div class='output co'>#> Splatter currently contains 11 simulations
+ <pre class="examples"><div class='input'><span class='fu'>listSims</span>()</div><div class='output co'>#> Splatter currently contains 12 simulations
#>
#> Splat (splat)
-#> DOI: GitHub:
+#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added.
#>
#> Splat Single (splatSingle)
-#> DOI: GitHub:
+#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> The Splat simulation with a single population.
#>
#> Splat Groups (splatGroups)
-#> DOI: GitHub:
+#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution.
#>
#> Splat Paths (splatPaths)
-#> DOI: GitHub:
+#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways.
#>
#> Simple (simple)
-#> DOI: GitHub:
+#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> A simple simulation with gamma means and negative binomial counts.
#>
#> Lun (lun)
@@ -151,13 +151,17 @@ displayed.</p>
#> Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.
#>
#> Lun 2 (lun2)
-#> DOI: 10.1101/073973 GitHub: MarioniLab/PlateEffects2016
+#> DOI: 10.1093/biostatistics/kxw055 GitHub: MarioniLab/PlateEffects2016
#> Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.
#>
#> scDD (scDD)
#> DOI: 10.1186/s13059-016-1077-y GitHub: kdkorthauer/scDD
#> The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.
#>
+#> BASiCS (BASiCS)
+#> DOI: 10.1371/journal.pcbi.1004333 GitHub: catavallejos/BASiCS
+#> The BASiCS simulation is based on a bayesian model used to deconvolve biological and technical variation and includes spike-ins and batch effects.
+#>
#> mfa (mfa)
#> DOI: 10.12688/wellcomeopenres.11087.1 GitHub: kieranrcampbell/mfa
#> The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
index 45a0e132d172bd313e7df72664db785261ed9e05..b4caa06e495f89049b38e68256c146e8484b6120 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -154,8 +154,8 @@ some genes or cells may be simulated multiple times.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Lun ATL, Marioni JC. Overcoming confounding plate effects in differential
-expression analyses of single-cell RNA-seq data. bioRxiv (2016).</p>
-<p>Paper: <a href='dx.doi.org/10.1101/073973'>dx.doi.org/10.1101/073973</a></p>
+expression analyses of single-cell RNA-seq data. Biostatistics (2017).</p>
+<p>Paper: <a href='dx.doi.org/10.1093/biostatistics/kxw055'>dx.doi.org/10.1093/biostatistics/kxw055</a></p>
<p>Code: <a href='https://github.com/MarioniLab/PlateEffects2016'>https://github.com/MarioniLab/PlateEffects2016</a></p>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 4d3d97cd872674d7b8ac41b6fd430e77fa6eb8e0..d616dc41eca3b506b56ed44d6a7d2c4e0b58bdac 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -146,7 +146,7 @@ for more details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 80751
+#> 2000 40 736969
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index 86367e0bb4179d6ec5e7f6919ec418f9748ef277..b43414b65a219a848445f1e94afefd0396f2d7f2 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -147,7 +147,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 80751
+#> 2000 40 736969
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
index f4a4e70af542d39e7fd1ae5f96078a8115ba9684..251cb3170c7793aade3520a787c2c3411b4acf52 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -106,7 +106,9 @@
Params subtypes.</p>
- <pre class="usage"><span class='fu'>newLun2Params</span>(<span class='no'>...</span>)
+ <pre class="usage"><span class='fu'>newBASiCSParams</span>(<span class='no'>...</span>)
+
+<span class='fu'>newLun2Params</span>(<span class='no'>...</span>)
<span class='fu'>newLunParams</span>(<span class='no'>...</span>)
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index 60f7ec4bf34ab36f4a50ea70f7f269b1bb3a5b80..97e7ff6a611b1e15d97df595839dc584064b0029 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -148,7 +148,7 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 80751
+#> 2000 40 736969
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 99335c81d2b59cea9716a897ff877b6b8bf887f7..d8975e913a431d10446f27806a522837fa53aa8c 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -107,6 +107,9 @@
<pre class="usage"><span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+<span class='co'># S4 method for BASiCSParams</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
<span class='co'># S4 method for Lun2Params</span>
<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
@@ -157,7 +160,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 80751
+#> 100 100 736969
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index fce88df4cb077ae9e146819f48ea87d99bfb503b..72d6c08ee1b49d80cc593c4ebb0fd8cfad2e8a93 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -146,7 +146,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (Genes) (Cells) [Seed]
-#> 10000 100 80751
+#> 10000 100 736969
#>
#> 3 additional parameters
#>
@@ -164,7 +164,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 80751
+#> 1000 50 736969
#>
#> 3 additional parameters
#>
@@ -182,7 +182,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 80751
+#> 1000 50 736969
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 4b84b6729feb6a544eb9cf305f59a0e9c76ad8ab..43fa74cd6854f6647b848f5d544344cdae30b09f 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -149,7 +149,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 80751
+#> 2000 40 736969
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 93bca84e612a8ad0975e6d8600f9d0b841b9e4de..9f05e80243496b1dba1b35239aefe9867acc0e4a 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -149,7 +149,7 @@ containing count data to estimate parameters from.</p></td>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 80751
+#> 2000 40 736969
#>
#> 27 additional parameters
#>
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index 85d30845689ac5af5f256576e1f8b912cb9c5c72..28ffcac03953ae094e8a8a1dbfba4e7a4cb1f17a 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -211,6 +211,13 @@ steps. These are stored in the <code><a href='http://www.rdocumentation.org/pack
in order to differentiate them from the values added by analysis packages
which typically use <code>underscore_naming</code>.</p>
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA
+sequencing data. Genome Biology (2017).</p>
+<p>Paper: <a href='10.1186/s13059-017-1305-0'>10.1186/s13059-017-1305-0</a></p>
+<p>Code: <a href='https://github.com/Oshlack/splatter'>https://github.com/Oshlack/splatter</a></p>
+
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<p><code><a href='splatSimLibSizes.html'>splatSimLibSizes</a></code>, <code><a href='splatSimGeneMeans.html'>splatSimGeneMeans</a></code>,
@@ -245,6 +252,8 @@ which typically use <code>underscore_naming</code>.</p>
<li><a href="#details">Details</a></li>
+ <li><a href="#references">References</a></li>
+
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 236c83c1bc918da684a9a17b3ae045ada6e97e6d..552d74d58c8cf57bff21794fc268d57f54183678 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -127,19 +127,19 @@ Error (RMSE) for the various properties and ranks them.</p>
<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 2.338299 NaN 1 2.392073 NaN
-#> 2 Splat Variance 11.506849 NaN 1 10.222706 NaN
-#> 3 Splat ZerosGene 30.000000 NaN 1 38.780000 NaN
-#> 4 Splat MeanVar 9.588721 NaN 1 11.820910 NaN
-#> 5 Splat MeanZeros 45.000000 NaN 1 42.060000 NaN
-#> 6 Splat LibSize 55543.500000 NaN 1 58282.850000 NaN
+#> 1 Splat Mean 2.757589 NaN 1 2.651957 NaN
+#> 2 Splat Variance 10.467288 NaN 1 10.272985 NaN
+#> 3 Splat ZerosGene 40.000000 NaN 1 44.935000 NaN
+#> 4 Splat MeanVar 9.682925 NaN 1 12.193247 NaN
+#> 5 Splat MeanZeros 45.000000 NaN 1 44.460000 NaN
+#> 6 Splat LibSize 56511.000000 NaN 1 59458.300000 NaN
#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 2.907697 NaN 1
-#> 2 1 12.865170 NaN 1
-#> 3 1 44.006818 NaN 1
-#> 4 1 14.953873 NaN 1
-#> 5 1 51.575673 NaN 1
-#> 6 1 59902.661935 NaN 1</div></pre>
+#> 1 1 3.182101 NaN 1
+#> 2 1 13.133714 NaN 1
+#> 3 1 48.428039 NaN 1
+#> 4 1 15.352203 NaN 1
+#> 5 1 53.898052 NaN 1
+#> 6 1 61094.139540 NaN 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/zinbEstimate.html b/docs/reference/zinbEstimate.html
index 29da734f978e6a770a8f471dfec8dcffd0546992..5bd42b014258b50ed8063b89c99d272c9e76ca1f 100644
--- a/docs/reference/zinbEstimate.html
+++ b/docs/reference/zinbEstimate.html
@@ -188,71 +188,11 @@ the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParam
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>zinbEstimate</span>(<span class='no'>sc_example_counts</span>)</div><div class='output co'>#> <span class='message'>Removing all zero genes...</span></div><div class='output co'>#> <span class='message'>Fitting model...</span></div><div class='output co'>#> <span class='message'>Create model:</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='output co'>#> <span class='message'>Initialize parameters:</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='output co'>#> <span class='message'>Optimize parameters:</span></div><div class='output co'>#> <span class='message'>Iteration 1</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 8.840 0.506 9.391 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 0.573 0.041 0.617 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 2</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -200962.486229372</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 6.414 0.345 6.790 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 0.616 0.025 0.643 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 3</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -196682.271688862</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 5.893 0.319 6.260 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 0.616 0.022 0.640 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 4</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -195719.09604664</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 4.808 0.251 5.075 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 0.600 0.013 0.615 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 5</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -195487.316905869</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 4.661 0.251 4.938 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 0.613 0.021 0.636 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 6</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -195438.512431125</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 4.363 0.219 4.594 </div><div class='output co'>#> <span class='message'>After right optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> user system elapsed
-#> 0.520 0.019 0.540 </div><div class='output co'>#> <span class='message'>After left optimization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -451653.610681949</span></div><div class='output co'>#> <span class='message'>Iteration 7</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -195429.243799278</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='input'><span class='no'>params</span></div><div class='output co'>#> A Params object of class ZINBParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'.
-#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 1973 40 80751
-#>
-#> 1 additional parameters
-#>
-#> Model:
-#> ZinbModel with 1973 features, 40 samples, 0 latent factors and 4027 parameters
-#>
-#> Model Design:
-#> (SAMPLES) (GENES)
-#> 1, 1, 1, 1,... 1, 1, 1, 1,...
-#>
-#> Model Offsets:
-#> (MU) (PI)
-#> 40 x 1973 matrix 40 x 1973 matrix
-#>
-#> Model Indices:
-#> (Sample Mu) (Gene Mu) (Sample Pi) (Gene Pi)
-#> 1 1 1 1
-#>
-#> Model Intercepts:
-#> (Sample Mu) (Gene Mu) (Sample Pi) (Gene Pi)
-#> TRUE TRUE TRUE TRUE
-#>
-#> Model Latent factors:
-#> (W)
-#> 40 x 0 matrix
-#>
-#> Model Coefficients:
-#> (SAMPLE MU)
-#> 2.92563256904469, 2.4987993436997, 2.58202880827954, 1.97900548945704,...
-#> (GENE MU)
-#> 3.47522026895399, 2.47301357124798, 3.24285373024315, 3.18809031726884,...
-#> (Latent Mu)
-#> 0 x 1973 matrix
-#> (SAMPLE PI)
-#> -0.71252392787508, -2.22126441075684, -0.171737848601069, -1.44324267217097,...
-#> (GENE PI)
-#> -0.0394934045621859, 0.702003614655306, 0.522586914345766, 0.331946546846606,...
-#> (Latent Pi)
-#> 0 x 1973 matrix
-#>
-#> Model Regularisation:
-#> (Sample Mu) (GENE MU) (Sample Pi) (GENE PI)
-#> 1 49.325 1 49.325
-#> (LATENT) (Latent coeffs) (ZETA) (Logit)
-#> 49.325 1 1973 0.001
-#> </div></pre>
+ <pre class="examples"><span class='co'># NOT RUN {</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'>zinbEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='no'>params</span>
+<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index f13d1c1c71ffa354053e1b16dd6eaf8cd5cd6948..6b287066109545df632ae56d85815133994a2152 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -1,6 +1,23 @@
\name{NEWS}
\title{News for Package \pkg{splatter}}
+\section{Version 1.1.8, Bioconductor 3.6 Release (2017-10-13)}{
+ \itemize{
+ \item{Now published in Genome Biology!}
+ \item{Converted to the SingleCellExperiment object}
+ \item{Added new simulations: BASiCS, mfa, PhenoPath, ZINB-WaVE}
+ \item{Added batch effects to the Splat simulation. This required a change
+ to the SplatParams object.}
+ \item{Improved scDD estimation}
+ \item{Added and improved comparison functions}
+ \item{Improved default Splat parameters and estimation}
+ \item{Improvements to the Lun2Params object}
+ \item{Added addGeneLength function}
+ \item{Updated simulation references}
+ \item{Various other minor updates and bug fixes}
+ }
+}
+
\section{Version 0.99.16, Bioconductor 3.5 Release (2017-04-23)}{
\itemize{
\item{Splatter is a package for the simple simulation of single-cell