From cd54e3e10bb2a44c1ec6f3bb3408e835cb85c7c5 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Wed, 2 May 2018 09:42:14 +1000
Subject: [PATCH] Bump bioc devel version
---
DESCRIPTION | 2 +-
NEWS.md | 4 ++++
docs/articles/index.html | 2 +-
docs/news/index.html | 7 +++++++
docs/reference/addGeneLengths.html | 12 ++++++------
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/sparseDCEstimate.html | 2 +-
docs/reference/splatEstimate.html | 2 +-
docs/reference/summariseDiff.html | 24 ++++++++++++------------
15 files changed, 42 insertions(+), 31 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 088ed38..f90032f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.4.0
+Version: 1.5.0
Date: 2018-05-02
Author: Luke Zappia
Authors@R:
diff --git a/NEWS.md b/NEWS.md
index 1296c6d..9ac04f6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+## Version 1.5.0 (2018-01-02)
+
+* Bioconductor 3.7 devel
+
# Version 1.4.0 (2018-01-02)
* Bioconductor 3.7 release
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 5f86ae4..1adddb0 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -96,7 +96,7 @@
</header>
<div class="page-header">
- <h1>Articles <small>version 1.4.0</small></h1>
+ <h1>Articles <small>version 1.5.0</small></h1>
</div>
<div class="row">
diff --git a/docs/news/index.html b/docs/news/index.html
index a6b4f6f..ea9dd90 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -103,6 +103,12 @@
</div>
<div class="contents">
+ <div class="section level2">
+<h2>Version 1.5.0 (2018-01-02)</h2>
+<ul>
+<li>Bioconductor 3.7 devel</li>
+</ul>
+</div>
<div class="section level1">
<h1>Version 1.4.0 (2018-01-02)</h1>
<ul>
@@ -510,6 +516,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#NA">1.5.0</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>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 2824c8c..592a186 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -156,12 +156,12 @@ vector.</p>
<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 0.00352990654436322 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)
+#> 1 Gene1 1.08758043949668 1146
+#> 2 Gene2 0.0748348805693826 2984
+#> 3 Gene3 4.39134549612356e-05 4834
+#> 4 Gene4 2.50529281404367 2495
+#> 5 Gene5 6.13362394694411 3769
+#> 6 Gene6 1.42330674557448 4022</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 1f02d45..a561dd4 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -100,7 +100,7 @@
<div class="page-header">
<h1>
Reference
- <small>version 1.4.0</small>
+ <small>version 1.5.0</small>
</h1>
</div>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 4cc19ab..576cfe2 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 346392
+#> 2000 40 171612
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index a5a00c2..eba1a78 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 346392
+#> 2000 40 171612
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index b77170a..5e0282e 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 346392
+#> 2000 40 171612
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 2c0b6b8..2566755 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -160,7 +160,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 346392
+#> 100 100 171612
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 32a180a..9eaa575 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 346392
+#> 10000 100 171612
#>
#> 3 additional parameters
#>
@@ -164,7 +164,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 346392
+#> 1000 50 171612
#>
#> 3 additional parameters
#>
@@ -182,7 +182,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 346392
+#> 1000 50 171612
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 999d96c..ea46323 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 346392
+#> 2000 40 171612
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index b7a7e90..82b4ad9 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 346392
+#> 500 20 171612
#>
#> 7 additional parameters
#>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 294036e..0d4661a 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 346392
+#> 2000 40 171612
#>
#> 28 additional parameters
#>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 3651d2e..51d407f 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 2.431092 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
+#> 1 Splat Mean 2.617539 NaN 1 2.620761 NaN
+#> 2 Splat Variance 11.320287 NaN 1 10.223665 NaN
+#> 3 Splat ZerosGene 35.000000 NaN 1 41.665000 NaN
+#> 4 Splat MeanVar 10.533179 NaN 1 12.061862 NaN
+#> 5 Splat MeanZeros 45.000000 NaN 1 43.805000 NaN
+#> 6 Splat LibSize 59620.000000 NaN 1 62014.200000 NaN
#> MAERank RMSE RMSEScaled RMSERank
-#> 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>
+#> 1 1 3.164726 NaN 1
+#> 2 1 12.986116 NaN 1
+#> 3 1 45.973090 NaN 1
+#> 4 1 15.097781 NaN 1
+#> 5 1 53.529198 NaN 1
+#> 6 1 63276.140327 NaN 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
--
GitLab