From d594208128e9ae6ccdd73a9c890c9bd31db138e2 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Wed, 31 Jan 2018 08:37:11 +1100
Subject: [PATCH] Bump version number
---
DESCRIPTION | 4 ++--
NEWS.md | 7 +++++++
docs/articles/index.html | 2 +-
docs/articles/splatter.html | 2 +-
docs/index.html | 2 --
docs/reference/addGeneLengths.html | 16 ++++++++--------
docs/reference/index.html | 2 +-
docs/reference/lunEstimate.html | 2 +-
docs/reference/mfaEstimate.html | 2 +-
docs/reference/phenoEstimate.html | 2 +-
docs/reference/setParam.html | 2 +-
docs/reference/setParams.html | 6 +++---
docs/reference/simpleEstimate.html | 2 +-
docs/reference/splatEstimate.html | 2 +-
docs/reference/summariseDiff.html | 24 ++++++++++++------------
15 files changed, 41 insertions(+), 36 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 0a1aa0a..48792b8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.3.1
-Date: 2018-01-03
+Version: 1.3.2
+Date: 2018-01-31
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 91b5743..fd2f279 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+## Version 1.3.2 (2018-01-31)
+
+* Fix QC names that have been changed in scater
+* Move scater to Imports and add scater version
+* Remove lingering references to SCESets
+* Add more tests
+
## Version 1.3.1 (2018-01-03)
* Fix error in vignette caused by changes in scater
diff --git a/docs/articles/index.html b/docs/articles/index.html
index d95fc09..2825f7a 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -96,7 +96,7 @@
</header>
<div class="page-header">
- <h1>Articles <small>version 1.3.1</small></h1>
+ <h1>Articles <small>version 1.3.2</small></h1>
</div>
<div class="row">
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index 3b44f7e..c190002 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">2018-01-30</h4>
+ <h4 class="date">2018-01-31</h4>
</div>
diff --git a/docs/index.html b/docs/index.html
index c87b1af..12d07cc 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -109,8 +109,6 @@ biocLite("splatter")</code></pre>
<div class="col-md-3" id="sidebar">
<h2>Links</h2>
<ul class="list-unstyled">
-<li>Download from BIOC at <br><a href="https://www.bioconductor.org/packages/splatter">https://​www.bioconductor.org/​packages/​splatter</a>
-</li>
<li>Browse source code at <br><a href="https://github.com/Oshlack/splatter">https://​github.com/​Oshlack/​splatter</a>
</li>
<li>Report a bug at <br><a href="https://github.com/Oshlack/splatter/issues">https://​github.com/​Oshlack/​splatter/​issues</a>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 55f294b..46c6a38 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 0.0370520 3077
-#> 2 Gene2 5.1457391 1099
-#> 3 Gene3 0.2357753 811
-#> 4 Gene4 0.4452486 3692
-#> 5 Gene5 0.1680624 3066
-#> 6 Gene6 0.9869200 1228</div><div class='input'># Sample method (human coding genes)
+#> Gene GeneMean Length
+#> <factor> <numeric> <numeric>
+#> 1 Gene1 2.81785069 5006
+#> 2 Gene2 0.47511411 3987
+#> 3 Gene3 0.05283592 5927
+#> 4 Gene4 1.89846584 3028
+#> 5 Gene5 0.13744696 1926
+#> 6 Gene6 4.97783720 2296</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 5b7eef7..f516a45 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -100,7 +100,7 @@
<div class="page-header">
<h1>
Reference
- <small>version 1.3.1</small>
+ <small>version 1.3.2</small>
</h1>
</div>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index bd18606..f81c760 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 603800
+#> 2000 40 490089
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index ab17ffe..9503a67 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 603800
+#> 2000 40 490089
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index 423f5f1..1fc42da 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 603800
+#> 2000 40 490089
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 0cb1cad..750924c 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -160,7 +160,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 603800
+#> 100 100 490089
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 0c09452..37528b7 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 603800
+#> 10000 100 490089
#>
#> 3 additional parameters
#>
@@ -164,7 +164,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 603800
+#> 1000 50 490089
#>
#> 3 additional parameters
#>
@@ -182,7 +182,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 603800
+#> 1000 50 490089
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 7fc4405..ae8d50a 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 603800
+#> 2000 40 490089
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 7059e3c..49dd923 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -152,7 +152,7 @@ containing count data to estimate parameters from.</p></td>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 603800
+#> 2000 40 490089
#>
#> 27 additional parameters
#>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index c0fb1a0..5403c36 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 3.545552e+00 NaN 1 3.129809e+00 NaN
-#> 2 Splat Variance 7.591704e-02 NaN 1 1.200872e-01 NaN
-#> 3 Splat ZerosGene 3.500000e+01 NaN 1 4.185500e+01 NaN
-#> 4 Splat MeanVar 4.092154e-01 NaN 1 4.692433e-01 NaN
-#> 5 Splat MeanZeros 4.500000e+01 NaN 1 4.415500e+01 NaN
-#> 6 Splat LibSize 6.258000e+04 NaN 1 6.246590e+04 NaN
+#> 1 Splat Mean 3.321288e+00 NaN 1 2.979458e+00 NaN
+#> 2 Splat Variance 8.683727e-02 NaN 1 1.405292e-01 NaN
+#> 3 Splat ZerosGene 3.500000e+01 NaN 1 4.170500e+01 NaN
+#> 4 Splat MeanVar 3.967063e-01 NaN 1 4.645264e-01 NaN
+#> 5 Splat MeanZeros 4.500000e+01 NaN 1 4.350500e+01 NaN
+#> 6 Splat LibSize 5.777350e+04 NaN 1 5.801215e+04 NaN
#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.498988e+00 NaN 1
-#> 2 1 1.702264e-01 NaN 1
-#> 3 1 4.627229e+01 NaN 1
-#> 4 1 5.756617e-01 NaN 1
-#> 5 1 5.414541e+01 NaN 1
-#> 6 1 6.399102e+04 NaN 1</div></pre>
+#> 1 1 3.344893e+00 NaN 1
+#> 2 1 1.900083e-01 NaN 1
+#> 3 1 4.601331e+01 NaN 1
+#> 4 1 5.744173e-01 NaN 1
+#> 5 1 5.298561e+01 NaN 1
+#> 6 1 5.913981e+04 NaN 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
--
GitLab