diff --git a/DESCRIPTION b/DESCRIPTION
index c92139a5cd0fb74bb28bb9505bed020ae50dba01..088ed38d3f99e6f8bc9183f9bb428b55b778ff42 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.5.0
-Date: 2018-04-30
+Version: 1.4.0
+Date: 2018-05-02
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 0ef87197162ba24e3d534c625f4167e4f5ba23c7..1296c6dd004657de55f7d5d52b8c32dd93b7e907 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# Version 1.4.0 (2018-01-02)
+
+* Bioconductor 3.7 release
+
## Version 1.3.6 (2018-04-30)
* Set seed in sparseDCEstimate tests
diff --git a/docs/articles/index.html b/docs/articles/index.html
index b16f949f96fd2f4b10f4fc579557bfad55cfc70f..5f86ae470470f4222c1b197749308ac6e3961f73 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -96,7 +96,7 @@
</header>
<div class="page-header">
- <h1>Articles <small>version 1.3.6</small></h1>
+ <h1>Articles <small>version 1.4.0</small></h1>
</div>
<div class="row">
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index 0887fa9e91ec538ac96f290b6aa46c0a1cfb696c..92425d11a47c49fd5d6739e30bded4e453bdd38d 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">2018-04-30</h4>
+ <h4 class="date">2018-05-02</h4>
</div>
@@ -322,7 +322,7 @@
##
## Global:
## (Genes) (Cells) [Seed]
-## 10000 100 778289
+## 10000 100 498429
##
## 28 additional parameters
##
@@ -355,8 +355,8 @@
## 0.1 60
##
## Dropout:
-## [Present] (Midpoint) (Shape)
-## FALSE 0 -1
+## [Type] (Midpoint) (Shape)
+## none 0 -1
##
## Paths:
## [From] [Length] [Skew] [Non-linear]
@@ -395,7 +395,7 @@
##
## Global:
## (GENES) (Cells) [Seed]
-## 8000 100 778289
+## 8000 100 498429
##
## 28 additional parameters
##
@@ -428,8 +428,8 @@
## 0.1 60
##
## Dropout:
-## [Present] (Midpoint) (Shape)
-## FALSE 0 -1
+## [Type] (Midpoint) (Shape)
+## none 0 -1
##
## Paths:
## [From] [Length] [Skew] [Non-linear]
@@ -495,7 +495,7 @@
<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" data-line-number="1">sim</a></code></pre></div>
<pre><code>## class: SingleCellExperiment
## dim: 1000 40
-## metadata(1): params
+## metadata(1): Params
## assays(6): BatchCellMeans BaseCellMeans ... TrueCounts counts
## rownames(1000): Gene1 Gene2 ... Gene999 Gene1000
## rowData names(4): Gene BaseGeneMean OutlierFactor GeneMean
@@ -507,33 +507,33 @@
<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" data-line-number="1"><span class="co"># Access the counts</span></a>
<a class="sourceLine" id="cb78-2" 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 4 6 0 0
-## Gene2 0 6 0 1 0
-## Gene3 0 0 0 0 0
-## Gene4 2 0 0 0 0
-## Gene5 48 515 97 176 11</code></pre>
+## 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="cb80"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb80-1" data-line-number="1"><span class="co"># Information about genes</span></a>
<a class="sourceLine" id="cb80-2" 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 2.62549353556827 1 2.62549353556827
-## 2 Gene2 4.81434700182375 1 4.81434700182375
-## 3 Gene3 0.495916446978038 1 0.495916446978038
-## 4 Gene4 34.1648904749076 1 34.1648904749076
-## 5 Gene5 24.7045533636413 1 24.7045533636413
-## 6 Gene6 250.903326326503 1 250.903326326503</code></pre>
+## 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="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" data-line-number="1"><span class="co"># Information about cells</span></a>
<a class="sourceLine" id="cb82-2" 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 954966.951755734
-## Cell2 Cell2 Batch1 405289.957543236
-## Cell3 Cell3 Batch1 584037.74996489
-## Cell4 Cell4 Batch1 602796.965710327
-## Cell5 Cell5 Batch1 87301.1571607906
-## Cell6 Cell6 Batch1 470868.325224977</code></pre>
+## 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="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
<a class="sourceLine" id="cb84-2" 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"
@@ -541,11 +541,11 @@
<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"># Example of cell means matrix</span></a>
<a class="sourceLine" id="cb86-2" 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 5.858361e-03 2.084916e+00 1.181249e+01 5.295042e-04 3.916082e-01
-## Gene2 5.880603e-10 1.013736e+01 1.861441e-04 3.629131e-01 1.743725e-05
-## Gene3 1.673555e-09 8.432645e-04 9.257897e-06 2.886216e-01 4.932245e-21
-## Gene4 6.088198e-01 1.685011e-06 1.528356e-17 2.186295e-01 3.857391e-02
-## Gene5 4.210456e+01 5.108598e+02 9.006138e+01 1.578927e+02 1.056544e+01</code></pre>
+## 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>
<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="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
<a class="sourceLine" id="cb88-2" 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>
@@ -657,7 +657,7 @@
<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="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
-<pre><code>## Splatter currently contains 12 simulations
+<pre><code>## Splatter currently contains 13 simulations
##
## Splat (splat)
## DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
@@ -705,7 +705,11 @@
##
## 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>
+## The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.
+##
+## SparseDC (sparseDC)
+## 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="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" 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">
@@ -801,6 +805,13 @@
<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>
+<tr class="odd">
+<td align="left">SparseDC</td>
+<td align="left">sparseDC</td>
+<td align="left">10.1093/nar/gkx1113</td>
+<td align="left">cran/SparseDC</td>
+<td align="left">The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.</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>
@@ -815,21 +826,21 @@
<pre><code>## DataFrame with 6 rows and 3 columns
## Gene GeneMean Length
## <factor> <numeric> <numeric>
-## 1 Gene1 0.952295922769918 1496
-## 2 Gene2 2.87873968030232 716
-## 3 Gene3 0.0135557245970668 4430
-## 4 Gene4 0.00368760310168385 2284
-## 5 Gene5 0.56378066886752 3537
-## 6 Gene6 3.19737947404623 2187</code></pre>
+## 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>
<p>We can then use <code>scater</code> to calculate TPM:</p>
<div class="sourceCode" id="cb108"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb108-1" 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="cb108-2" 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 0.05053290 0.000000 0.00000000 0.05102276 0.05145083
-## Gene2 0.21116541 0.418942 0.52430665 0.00000000 0.53750310
-## Gene3 0.00000000 0.000000 0.00000000 0.00000000 0.00000000
-## Gene4 0.03309861 0.000000 0.00000000 0.00000000 0.00000000
-## Gene5 0.00000000 0.000000 0.02122723 0.02158045 0.00000000</code></pre>
+<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>
<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">
@@ -913,13 +924,13 @@
<h1 class="hasAnchor">
<a href="#session-information" class="anchor"></a>Session information</h1>
<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="kw">sessionInfo</span>()</a></code></pre></div>
-<pre><code>## R version 3.5.0 beta (2018-04-10 r74581)
-## Platform: x86_64-apple-darwin16.7.0 (64-bit)
+<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
##
## Matrix products: default
-## BLAS: /Users/luke.zappia/r-devel/lib/R/lib/libRblas.dylib
-## LAPACK: /Users/luke.zappia/r-devel/lib/R/lib/libRlapack.dylib
+## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
+## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
@@ -929,50 +940,51 @@
## [8] methods base
##
## other attached packages:
-## [1] scater_1.7.15 ggplot2_2.2.1
-## [3] splatter_1.3.3.9010 SingleCellExperiment_1.1.3
-## [5] SummarizedExperiment_1.9.16 DelayedArray_0.5.30
-## [7] BiocParallel_1.13.3 matrixStats_0.53.1
-## [9] Biobase_2.39.2 GenomicRanges_1.31.23
-## [11] GenomeInfoDb_1.15.5 IRanges_2.13.28
-## [13] S4Vectors_0.17.41 BiocGenerics_0.25.3
+## [1] scater_1.8.0 ggplot2_2.2.1
+## [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_2.14.0
+## [13] S4Vectors_0.18.0 BiocGenerics_0.26.0
##
## loaded via a namespace (and not attached):
-## [1] viridis_0.5.1 edgeR_3.21.9
-## [3] viridisLite_0.3.0 splines_3.5.0
-## [5] DelayedMatrixStats_1.1.12 shiny_1.0.5
-## [7] assertthat_0.2.0 highr_0.6
-## [9] sp_1.2-7 GenomeInfoDbData_1.1.0
-## [11] vipor_0.4.5 yaml_2.1.18
-## [13] pillar_1.2.1 backports_1.1.2
-## [15] lattice_0.20-35 glue_1.2.0
-## [17] limma_3.35.14 digest_0.6.15
-## [19] XVector_0.19.9 checkmate_1.8.6
-## [21] colorspace_1.3-2 cowplot_0.9.2
-## [23] htmltools_0.3.6 httpuv_1.3.6.2
-## [25] Matrix_1.2-14 plyr_1.8.4
-## [27] pkgconfig_2.0.1 zlibbioc_1.25.0
-## [29] xtable_1.8-2 scales_0.5.0
-## [31] tibble_1.4.2 lazyeval_0.2.1
-## [33] crayon_1.3.4 survival_2.41-3
-## [35] magrittr_1.5 mime_0.5
-## [37] evaluate_0.10.1 MASS_7.3-49
-## [39] beeswarm_0.2.3 shinydashboard_0.7.0
-## [41] tools_3.5.0 fitdistrplus_1.0-9
-## [43] data.table_1.10.4-3 stringr_1.3.0
-## [45] Rhdf5lib_1.1.5 munsell_0.4.3
-## [47] locfit_1.5-9.1 bindrcpp_0.2.2
-## [49] akima_0.6-2 compiler_3.5.0
-## [51] rlang_0.2.0 rhdf5_2.23.7
-## [53] grid_3.5.0 RCurl_1.95-4.10
-## [55] tximport_1.7.14 rjson_0.2.15
-## [57] labeling_0.3 bitops_1.0-6
-## [59] rmarkdown_1.9 gtable_0.2.0
-## [61] reshape2_1.4.3 R6_2.2.2
-## [63] gridExtra_2.3 knitr_1.20
-## [65] dplyr_0.7.4 bindr_0.1.1
-## [67] rprojroot_1.3-2 stringi_1.1.7
-## [69] ggbeeswarm_0.6.0 Rcpp_0.12.16</code></pre>
+## [1] viridis_0.5.1 edgeR_3.22.0
+## [3] splines_3.5.0 viridisLite_0.3.0
+## [5] DelayedMatrixStats_1.2.0 shiny_1.0.5
+## [7] assertthat_0.2.0 highr_0.6
+## [9] sp_1.2-7 GenomeInfoDbData_1.1.0
+## [11] vipor_0.4.5 yaml_2.1.19
+## [13] pillar_1.2.2 backports_1.1.2
+## [15] lattice_0.20-35 glue_1.2.0
+## [17] limma_3.36.0 digest_0.6.15
+## [19] promises_1.0.1 XVector_0.20.0
+## [21] checkmate_1.8.6 colorspace_1.3-2
+## [23] cowplot_0.9.2 htmltools_0.3.6
+## [25] httpuv_1.4.1 Matrix_1.2-14
+## [27] plyr_1.8.4 pkgconfig_2.0.1
+## [29] zlibbioc_1.26.0 xtable_1.8-2
+## [31] scales_0.5.0 later_0.7.2
+## [33] tibble_1.4.2 lazyeval_0.2.1
+## [35] crayon_1.3.4 survival_2.42-3
+## [37] magrittr_1.5 mime_0.5
+## [39] evaluate_0.10.1 MASS_7.3-50
+## [41] beeswarm_0.2.3 shinydashboard_0.7.0
+## [43] tools_3.5.0 fitdistrplus_1.0-9
+## [45] data.table_1.11.0 stringr_1.3.0
+## [47] Rhdf5lib_1.2.0 munsell_0.4.3
+## [49] locfit_1.5-9.1 bindrcpp_0.2.2
+## [51] akima_0.6-2 compiler_3.5.0
+## [53] rlang_0.2.0 rhdf5_2.24.0
+## [55] grid_3.5.0 RCurl_1.95-4.10
+## [57] tximport_1.8.0 rjson_0.2.15
+## [59] labeling_0.3 bitops_1.0-6
+## [61] rmarkdown_1.9 gtable_0.2.0
+## [63] reshape2_1.4.3 R6_2.2.2
+## [65] gridExtra_2.3 knitr_1.20
+## [67] dplyr_0.7.4 bindr_0.1.1
+## [69] rprojroot_1.3-2 stringi_1.1.7
+## [71] ggbeeswarm_0.6.0 Rcpp_0.12.16</code></pre>
</div>
</div>
</div>
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diff --git a/docs/news/index.html b/docs/news/index.html
index 642f9d0892a5b6f1bb75bd03f6cb265f97301471..a6b4f6fb29007fff5e293dd945781ed50192cddd 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -103,13 +103,18 @@
</div>
<div class="contents">
- <div class="section level2">
+ <div class="section level1">
+<h1>Version 1.4.0 (2018-01-02)</h1>
+<ul>
+<li>Bioconductor 3.7 release</li>
+</ul>
+<div class="section level2">
<h2>Version 1.3.6 (2018-04-30)</h2>
<ul>
<li>Set seed in sparseDCEstimate tests</li>
</ul>
</div>
- <div class="section level2">
+<div class="section level2">
<h2>Version 1.3.5 (2018-04-25)</h2>
<ul>
<li>Replace dropout.present with dropout.type in SplatParams
@@ -119,7 +124,7 @@
</li>
</ul>
</div>
- <div class="section level2">
+<div class="section level2">
<h2>Version 1.3.4 (2018-04-19)</h2>
<ul>
<li>Add option to use a normal distribution for library sizes in Splat simulations</li>
@@ -148,13 +153,13 @@
</ul>
</div>
</div>
- <div class="section level2">
+<div class="section level2">
<h2>Version 1.3.3 (2018-03-27)</h2>
<ul>
<li>Fix parameter passing bug in scDDEstimate</li>
</ul>
</div>
- <div class="section level2">
+<div class="section level2">
<h2>Version 1.3.2 (2018-01-31)</h2>
<ul>
<li>Fix QC names that have been changed in scater</li>
@@ -163,29 +168,30 @@
<li>Add more tests</li>
</ul>
</div>
- <div class="section level2">
+<div class="section level2">
<h2>Version 1.3.1 (2018-01-03)</h2>
<ul>
<li>Fix error in vignette caused by changes in scater</li>
</ul>
</div>
- <div class="section level2">
+<div class="section level2">
<h2>Version 1.3.0 (2017-10-13)</h2>
<ul>
<li>Bioconductor 3.7 devel</li>
</ul>
</div>
- <div class="section level2">
+<div class="section level2">
<h2>Version 1.2.2 (2018-03-27)</h2>
<ul>
<li>Fix parameter passing bug in scDDEstimate</li>
</ul>
</div>
- <div class="section level2">
+<div class="section level2">
<h2>Version 1.2.1 (2017-11-23)</h2>
<ul>
<li>Fix zinbwave installation error</li>
</ul>
+</div>
</div>
<div class="section level1">
<h1>Version 1.2.0 (2017-10-30)</h1>
@@ -504,15 +510,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#NA">1.3.6</a></li>
- <li><a href="#NA">1.3.5</a></li>
- <li><a href="#NA">1.3.4</a></li>
- <li><a href="#NA">1.3.3</a></li>
- <li><a href="#NA">1.3.2</a></li>
- <li><a href="#NA">1.3.1</a></li>
- <li><a href="#NA">1.3.0</a></li>
- <li><a href="#NA">1.2.2</a></li>
- <li><a href="#NA">1.2.1</a></li>
+ <li><a href="#NA">1.4.0</a></li>
<li><a href="#NA">1.2.0</a></li>
<li><a href="#NA">1.0.0</a></li>
<li><a href="#NA">0.99.0</a></li>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index f87091d73845c86c7943094de09c036bbaa690e0..2824c8ca4588637987429e5c26569edff0564129 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 0.734025020368755 8478
-#> 2 Gene2 1.72488562332675 4683
-#> 3 Gene3 0.602236437812367 3861
-#> 4 Gene4 0.279058870872173 1711
-#> 5 Gene5 0.00808100968671002 3209
-#> 6 Gene6 4.60422371602675 1349</div><div class='input'># Sample method (human coding genes)
+#> Gene GeneMean Length
+#> <factor> <numeric> <numeric>
+#> 1 Gene1 0.00352990654436322 6438
+#> 2 Gene2 1.4310789627999 1977
+#> 3 Gene3 2.97303433883906 1141
+#> 4 Gene4 1.68672596847337 5683
+#> 5 Gene5 0.623963523718446 2098
+#> 6 Gene6 0.000108169127516354 5211</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/index.html b/docs/reference/index.html
index f0a5f140d85cd9949a3e9cd3e4d85b633fd67751..1f02d4542bd1f2fa5910943f7f4cc50aa9595766 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -100,7 +100,7 @@
<div class="page-header">
<h1>
Reference
- <small>version 1.3.6</small>
+ <small>version 1.4.0</small>
</h1>
</div>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 9e3f6bb3c88b4eb509a48f64f2fa6199d5b1cad9..4cc19abe991fc4036b507476f4c1ffffbabfe705 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -149,7 +149,7 @@ for more details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 239255
+#> 2000 40 346392
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index 806172e1400834cc304469ca27592253b3c6a04a..a5a00c208ba4eaea785795d048e71cef7c077cb2 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -150,7 +150,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 239255
+#> 2000 40 346392
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index c426f249136f1315a8033bd3f33a11324b301b9a..b77170a6e63897391873909a5de3115d2b8025bd 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -151,7 +151,7 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 239255
+#> 2000 40 346392
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index c744aff2fe91ab9ffe0f58204636dbf5b585c910..2c0b6b88faf62b238ae6fc83f902dfde0429ac89 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -160,7 +160,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 239255
+#> 100 100 346392
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index b1dd65fb7a6af30b047ca0dfb2ff9ca581fa838d..32a180a6ac1be06a3da5352c9ac190075946b598 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 239255
+#> 10000 100 346392
#>
#> 3 additional parameters
#>
@@ -164,7 +164,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 239255
+#> 1000 50 346392
#>
#> 3 additional parameters
#>
@@ -182,7 +182,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 239255
+#> 1000 50 346392
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index cde8accc8304e4ce376036958e7a3cf252f12800..999d96c1fd8e9fca0e9743cbdee7c5dc4e35b975 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -152,7 +152,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 239255
+#> 2000 40 346392
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index cb9edf34370a7e524e10a8414666632c680ca94a..b7a7e9051acfb98e9582874aaa6e948b36821cb5 100644
--- a/docs/reference/sparseDCEstimate.html
+++ b/docs/reference/sparseDCEstimate.html
@@ -174,7 +174,7 @@ input data. The counts are preprocessed using
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 500 20 239255
+#> 500 20 346392
#>
#> 7 additional parameters
#>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index ea70708fbbe60cade26d484c8bc82ef405eb9879..294036ee1e09f618affedc3f585bc08f5ad2cc52 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -151,7 +151,7 @@ containing count data to estimate parameters from.</p></td>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 239255
+#> 2000 40 346392
#>
#> 28 additional parameters
#>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 35b7468d66a336eec08dc06cf8db9e695211e090..3651d2e1c70e8cb79381bc5d63362bf174695b00 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -128,19 +128,19 @@ Error (RMSE) for the various properties and ranks them.</p>
#> <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 2.747262 NaN 1 2.687708 NaN
-#> 2 Splat Variance 12.048614 NaN 1 10.964929 NaN
-#> 3 Splat ZerosGene 40.000000 NaN 1 44.560000 NaN
-#> 4 Splat MeanVar 11.536097 NaN 1 12.817781 NaN
-#> 5 Splat MeanZeros 45.000000 NaN 1 44.735000 NaN
-#> 6 Splat LibSize 60309.000000 NaN 1 62775.150000 NaN
+#> 1 Splat Mean 2.431092 NaN 1 2.419012 NaN
+#> 2 Splat Variance 10.156587 NaN 1 9.597323 NaN
+#> 3 Splat ZerosGene 30.000000 NaN 1 38.525000 NaN
+#> 4 Splat MeanVar 8.766075 NaN 1 11.305514 NaN
+#> 5 Splat MeanZeros 40.000000 NaN 1 41.730000 NaN
+#> 6 Splat LibSize 62089.500000 NaN 1 59054.250000 NaN
#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.224377 NaN 1
-#> 2 1 13.890753 NaN 1
-#> 3 1 48.064020 NaN 1
-#> 4 1 15.970356 NaN 1
-#> 5 1 54.010879 NaN 1
-#> 6 1 63881.558662 NaN 1</div></pre>
+#> 1 1 2.947972 NaN 1
+#> 2 1 12.058784 NaN 1
+#> 3 1 43.461190 NaN 1
+#> 4 1 14.258312 NaN 1
+#> 5 1 51.490776 NaN 1
+#> 6 1 60072.826128 NaN 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>