[med-svn] [r-bioc-edger] 01/03: Imported Upstream version 3.8.2+dfsg
Andreas Tille
tille at debian.org
Mon Oct 20 16:09:50 UTC 2014
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tille pushed a commit to branch master
in repository r-bioc-edger.
commit 10b108d4c823cb7fdac32aa37069a6d764282243
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 20 13:00:00 2014 +0200
Imported Upstream version 3.8.2+dfsg
---
DESCRIPTION | 6 +++---
R/decidetestsDGE.R | 7 ++++---
inst/CITATION | 13 +++++++++++++
inst/doc/edgeR.pdf | Bin 48664 -> 48664 bytes
man/decidetestsDGE.Rd | 3 ++-
man/estimateGLMRobustDisp.Rd | 2 +-
6 files changed, 23 insertions(+), 8 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index dd553ea..4fcf5b6 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: edgeR
-Version: 3.8.0
-Date: 2014/10/10
+Version: 3.8.2
+Date: 2014/10/17
Title: Empirical analysis of digital gene expression data in R
Author: Yunshun Chen <yuchen at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Aaron Lun <alun at wehi.edu.au>, Xiaobei Zhou <xiaobei.zhou at uzh.ch>, Mark Robinson <mark.robinson at imls.uzh.ch>, Gordon Smyth <smyth at wehi.edu.au>
Maintainer: Yunshun Chen <yuchen at wehi.edu.au>, Mark Robinson <mark.robinson at imls.uzh.ch>, Davis McCarthy <dmccarthy at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>
@@ -15,4 +15,4 @@ biocViews: GeneExpression, Transcription, AlternativeSplicing,
TimeCourse, SAGE, Sequencing, ChIPSeq, RNASeq, BatchEffect,
MultipleComparison, Normalization, QualityControl
Description: Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with other types of genome-scale count data.
-Packaged: 2014-10-14 01:06:08 UTC; biocbuild
+Packaged: 2014-10-18 00:59:00 UTC; biocbuild
diff --git a/R/decidetestsDGE.R b/R/decidetestsDGE.R
index 09b9af0..88bd1ab 100644
--- a/R/decidetestsDGE.R
+++ b/R/decidetestsDGE.R
@@ -1,12 +1,13 @@
# DECIDETESTSDGE.R
-decideTestsDGE <- function(object,adjust.method="BH",p.value=0.05)
+decideTestsDGE <- function(object,adjust.method="BH",p.value=0.05,lfc=0)
## Accept or reject hypothesis tests across genes and contrasts
## Davis McCarthy
- ## 15 August 2010. Last modified 19 Jan 2012.
+ ## 15 August 2010. Last modified 17 Oct 2014 (Mark Robinson).
{
if(!is(object,"DGEExact") & !is(object,"DGELRT")) stop("Need DGEExact or DGELRT object") # Expects a DGEExact or DGELRT object
- decideTests(new("MArrayLM", list(p.value=object$table$PValue, coefficients=object$table$logFC)), method="separate", adjust.method=adjust.method, p.value=p.value)
+ decideTests(new("MArrayLM", list(p.value=object$table$PValue, coefficients=object$table$logFC)),
+ method="separate", adjust.method=adjust.method, p.value=p.value, lfc=lfc)
}
diff --git a/inst/CITATION b/inst/CITATION
index 4daae0d..1729cef 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -44,3 +44,16 @@ citEntry(
year = 2008,
textVersion = "Robinson MD and Smyth GK (2008). Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 9, 321-332"
)
+
+
+citEntry(
+ entry="article",
+ title = "Robustly detecting differential expression in RNA sequencing data using observation weights",
+ author = "Xiaobei Zhou and Helen Lindsay and Mark D Robinson",
+ journal = "Nucleic Acids Research",
+ volume = 42,
+ pages = "e91",
+ year = 2014,
+ textVersion = "Zhou X, Lindsay H, Robinson MD (2014). Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Research, 42(11), e91."
+)
+
diff --git a/inst/doc/edgeR.pdf b/inst/doc/edgeR.pdf
index a20e249..5f809ce 100644
Binary files a/inst/doc/edgeR.pdf and b/inst/doc/edgeR.pdf differ
diff --git a/man/decidetestsDGE.Rd b/man/decidetestsDGE.Rd
index f059d91..5fe522f 100644
--- a/man/decidetestsDGE.Rd
+++ b/man/decidetestsDGE.Rd
@@ -6,7 +6,7 @@ Classify a series of related differential expression statistics as up, down or n
A number of different multiple testing schemes are offered which adjust for multiple testing down the genes as well as across contrasts for each gene.
}
\usage{
-decideTestsDGE(object, adjust.method="BH", p.value=0.05)
+decideTestsDGE(object, adjust.method="BH", p.value=0.05, lfc=0)
}
\arguments{
\item{object}{\code{deDGElist} object, output from \code{exactTest},
@@ -16,6 +16,7 @@ decideTestsDGE(object, adjust.method="BH", p.value=0.05)
\item{adjust.method}{character string specifying p-value adjustment method. Possible values are \code{"none"}, \code{"BH"}, \code{"fdr"} (equivalent to \code{"BH"}), \code{"BY"} and \code{"holm"}. See \code{\link[stats]{p.adjust}} for details.}
\item{p.value}{numeric value between 0 and 1 giving the desired size of the test}
+ \item{lfc}{numeric value giving the desired absolute minimum log-fold-change}
}
\value{
An object of class \code{TestResults} (see \code{\link[limma:TestResults]{TestResults}}).
diff --git a/man/estimateGLMRobustDisp.Rd b/man/estimateGLMRobustDisp.Rd
index c1e1b58..cf4c927 100644
--- a/man/estimateGLMRobustDisp.Rd
+++ b/man/estimateGLMRobustDisp.Rd
@@ -40,7 +40,7 @@ Note: it is not necessary to first calculate the common, trended and tagwise dis
}
\references{
-Zhou X, Lindsay H and Robinson MD (2013) Robustly detecting differential expression in RNA sequencing data using observation weights \emph{in preparation}.
+Zhou X, Lindsay H, Robinson MD (2014). Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Research, 42(11), e91.
}
\author{Xiaobei Zhou, Mark D. Robinson}
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