From 065574a9b9936bc125fe92b24309e7176a40d6b3 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Mon, 30 Apr 2018 11:23:39 +1000
Subject: [PATCH] Set seed in sparseDCEstimate tests and bump ver
These would sometimes error due to sampling of example dataset
---
DESCRIPTION | 4 ++--
NEWS.md | 6 +++++-
R/sparseDC-estimate.R | 1 +
docs/articles/index.html | 2 +-
docs/articles/splatter.html | 2 +-
docs/news/index.html | 11 +++++++++--
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/sparseDCEstimate.html | 3 ++-
docs/reference/splatEstimate.html | 2 +-
docs/reference/summariseDiff.html | 24 ++++++++++++------------
man/sparseDCEstimate.Rd | 1 +
tests/testthat/test-sparseDCEstimate.R | 2 +-
19 files changed, 53 insertions(+), 39 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index f67bea7..0a61b2b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.3.5
-Date: 2018-04-25
+Version: 1.3.6
+Date: 2018-04-30
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 7f7748b..0ef8719 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,8 @@
-## Version 1.3.4 (2018-04-25)
+## Version 1.3.6 (2018-04-30)
+
+* Set seed in sparseDCEstimate tests
+
+## Version 1.3.5 (2018-04-25)
* Replace dropout.present with dropout.type in SplatParams
* Allows users to set dropout by experiment, batch, group or cell
diff --git a/R/sparseDC-estimate.R b/R/sparseDC-estimate.R
index 1439bcf..0c0f793 100644
--- a/R/sparseDC-estimate.R
+++ b/R/sparseDC-estimate.R
@@ -28,6 +28,7 @@
#' library(scater)
#' data("sc_example_counts")
#'
+#' set.seed(1)
#' conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
#'
#' params <- sparseDCEstimate(sc_example_counts[1:500, ], conditions,
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 088ab52..b16f949 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -96,7 +96,7 @@
</header>
<div class="page-header">
- <h1>Articles <small>version 1.3.5</small></h1>
+ <h1>Articles <small>version 1.3.6</small></h1>
</div>
<div class="row">
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index 7602e93..0887fa9 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">2018-04-25</h4>
+ <h4 class="date">2018-04-30</h4>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index b7ebc7e..642f9d0 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -104,7 +104,13 @@
<div class="contents">
<div class="section level2">
-<h2>Version 1.3.4 (2018-04-25)</h2>
+<h2>Version 1.3.6 (2018-04-30)</h2>
+<ul>
+<li>Set seed in sparseDCEstimate tests</li>
+</ul>
+</div>
+ <div class="section level2">
+<h2>Version 1.3.5 (2018-04-25)</h2>
<ul>
<li>Replace dropout.present with dropout.type in SplatParams
<ul>
@@ -498,7 +504,8 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#NA">1.3.4</a></li>
+ <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>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index b436347..f87091d 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 3.19721697566766 428
-#> 2 Gene2 0.316692135258865 2948
-#> 3 Gene3 2.90867080625693 1507
-#> 4 Gene4 7.5357203351493 6034
-#> 5 Gene5 5.92953185619191 1713
-#> 6 Gene6 3.78237895789214 2926</div><div class='input'># Sample method (human coding genes)
+#> 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)
</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 37647c5..f0a5f14 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -100,7 +100,7 @@
<div class="page-header">
<h1>
Reference
- <small>version 1.3.5</small>
+ <small>version 1.3.6</small>
</h1>
</div>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 7978288..9e3f6bb 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 33804
+#> 2000 40 239255
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index df646e1..806172e 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 33804
+#> 2000 40 239255
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index b19c096..c426f24 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 33804
+#> 2000 40 239255
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 7b675e5..c744aff 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -160,7 +160,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 33804
+#> 100 100 239255
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 24447c4..b1dd65f 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 33804
+#> 10000 100 239255
#>
#> 3 additional parameters
#>
@@ -164,7 +164,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 33804
+#> 1000 50 239255
#>
#> 3 additional parameters
#>
@@ -182,7 +182,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 33804
+#> 1000 50 239255
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 548b300..cde8acc 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 33804
+#> 2000 40 239255
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index 3ab9bb0..cb9edf3 100644
--- a/docs/reference/sparseDCEstimate.html
+++ b/docs/reference/sparseDCEstimate.html
@@ -164,6 +164,7 @@ input data. The counts are preprocessed using
<span class='fu'>library</span>(<span class='no'>scater</span>)
<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'>set.seed</span>(<span class='fl'>1</span>)
<span class='no'>conditions</span> <span class='kw'><-</span> <span class='fu'>sample</span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'>ncol</span>(<span class='no'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>sparseDCEstimate</span>(<span class='no'>sc_example_counts</span>[<span class='fl'>1</span>:<span class='fl'>500</span>, ], <span class='no'>conditions</span>,
@@ -173,7 +174,7 @@ input data. The counts are preprocessed using
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 500 20 33804
+#> 500 20 239255
#>
#> 7 additional parameters
#>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 4699daf..ea70708 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 33804
+#> 2000 40 239255
#>
#> 28 additional parameters
#>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index a1d0f60..35b7468 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 2.578921 NaN 1 2.526951 NaN
-#> 2 Splat Variance 11.923672 NaN 1 10.771444 NaN
-#> 3 Splat ZerosGene 35.000000 NaN 1 41.210000 NaN
-#> 4 Splat MeanVar 11.687919 NaN 1 12.429719 NaN
-#> 5 Splat MeanZeros 45.000000 NaN 1 42.440000 NaN
-#> 6 Splat LibSize 53750.500000 NaN 1 57352.550000 NaN
+#> 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
#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.056807 NaN 1
-#> 2 1 13.346501 NaN 1
-#> 3 1 45.518677 NaN 1
-#> 4 1 15.389141 NaN 1
-#> 5 1 51.924946 NaN 1
-#> 6 1 58750.990661 NaN 1</div></pre>
+#> 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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/man/sparseDCEstimate.Rd b/man/sparseDCEstimate.Rd
index 274d074..4d19581 100644
--- a/man/sparseDCEstimate.Rd
+++ b/man/sparseDCEstimate.Rd
@@ -50,6 +50,7 @@ See \code{\link{SparseDCParams}} for more details on the parameters.
library(scater)
data("sc_example_counts")
+set.seed(1)
conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
params <- sparseDCEstimate(sc_example_counts[1:500, ], conditions,
diff --git a/tests/testthat/test-sparseDCEstimate.R b/tests/testthat/test-sparseDCEstimate.R
index a34ac48..3bdc50b 100644
--- a/tests/testthat/test-sparseDCEstimate.R
+++ b/tests/testthat/test-sparseDCEstimate.R
@@ -4,8 +4,8 @@ library(scater)
data("sc_example_counts")
test_that("sparseDCEstimate works", {
+ set.seed(1)
conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
-
params <- sparseDCEstimate(sc_example_counts, conditions,
nclusters = 3)
expect_true(validObject(params))
--
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