[med-svn] [r-bioc-limma] 01/03: Imported Upstream version 3.22.1+dfsg
Andreas Tille
tille at debian.org
Fri Oct 24 21:33:15 UTC 2014
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tille pushed a commit to branch master
in repository r-bioc-limma.
commit 140fe49134558a5022cf792783d9c30194382f54
Author: Andreas Tille <tille at debian.org>
Date: Fri Oct 24 23:22:02 2014 +0200
Imported Upstream version 3.22.1+dfsg
---
DESCRIPTION | 6 +++---
NAMESPACE | 3 +++
R/geneset-romer.R | 17 +++++++++--------
inst/doc/changelog.txt | 6 ++++++
inst/doc/intro.pdf | Bin 46191 -> 46191 bytes
man/romer.Rd | 14 +++++++++-----
tests/limma-Tests.Rout.save | 2 +-
7 files changed, 31 insertions(+), 17 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index ea6a945..e9e786b 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: limma
-Version: 3.22.0
-Date: 2014/10/10
+Version: 3.22.1
+Date: 2014/10/20
Title: Linear Models for Microarray Data
Description: Data analysis, linear models and differential expression for microarray data.
Author: Gordon Smyth [cre,aut], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Natalie Thorne [ctb], Davis McCarthy [ctb], Di Wu [ctb], Yifang Hu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]
@@ -19,4 +19,4 @@ biocViews: ExonArray, GeneExpression, Transcription,
ProprietaryPlatforms, TwoChannel, RNASeq, BatchEffect,
MultipleComparison, Normalization, Preprocessing,
QualityControl
-Packaged: 2014-10-14 00:27:12 UTC; biocbuild
+Packaged: 2014-10-21 00:24:11 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index daf3545..226c493 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -34,6 +34,7 @@ S3method(avereps,EList)
S3method(avearrays,default)
S3method(avearrays,MAList)
S3method(avearrays,EList)
+S3method(camera,default)
S3method(cbind,MAList)
S3method(cbind,RGList)
S3method(cbind,EList)
@@ -64,6 +65,8 @@ S3method(merge,MAList)
S3method(merge,RGList)
S3method(merge,EList)
S3method(merge,EListRaw)
+S3method(roast,default)
+S3method(romer,default)
S3method(rbind,MAList)
S3method(rbind,RGList)
S3method(rbind,EList)
diff --git a/R/geneset-romer.R b/R/geneset-romer.R
index a258740..8af04bd 100644
--- a/R/geneset-romer.R
+++ b/R/geneset-romer.R
@@ -1,4 +1,5 @@
## ROMER.R
+romer <- function(y,...) UseMethod("romer")
ids2indices <- function(gene.sets, identifiers, remove.empty=TRUE)
# Make a list of gene identifiers into a list of indices for gene sets
@@ -12,23 +13,23 @@ ids2indices <- function(gene.sets, identifiers, remove.empty=TRUE)
index
}
-romer <- function(index,y,design,contrast=ncol(design),array.weights=NULL,block=NULL,correlation=NULL,set.statistic="mean",nrot=9999)
+romer.default <- function(y,index,design,contrast=ncol(design),array.weights=NULL,block=NULL,correlation=NULL,set.statistic="mean",nrot=9999,...)
# rotation mean-rank version of GSEA (gene set enrichment analysis) for linear models
# Gordon Smyth and Yifang Hu
-# 27 March 2009. Last modified 3 June 2010.
+# 27 March 2009. Last modified 20 October 2014.
{
set.statistic <- match.arg(set.statistic,c("mean","floormean","mean50"))
if(set.statistic=="mean50") {
- return(.romer.mean50(index=index,y=y,design=design,contrast=contrast,array.weights=array.weights,block=block,correlation=correlation,nrot=nrot))
+ return(.romer.mean50(y=y,index=index,design=design,contrast=contrast,array.weights=array.weights,block=block,correlation=correlation,nrot=nrot))
} else {
- return(.romer.mean.floormean(index=index,y=y,design=design,contrast=contrast,array.weights=array.weights,block=block,correlation=correlation,floor=(set.statistic=="floormean"),nrot=nrot))
+ return(.romer.mean.floormean(y=y,index=index,design=design,contrast=contrast,array.weights=array.weights,block=block,correlation=correlation,floor=(set.statistic=="floormean"),nrot=nrot))
}
}
-.romer.mean50 <- function(index,y,design,contrast=ncol(design),array.weights=NULL,block=NULL,correlation,nrot=9999)
+.romer.mean50 <- function(y,index,design,contrast=ncol(design),array.weights=NULL,block=NULL,correlation,nrot=9999)
# rotation-mean50-rank version of GSEA (gene set enrichment analysis) for linear models
# Gordon Smyth and Yifang Hu
-# 27 March 2009. Last modified 15 Sep 2009.
+# 27 March 2009. Last modified 20 October 2014.
{
# Check input arguments
if(!is.list(index)) index <- list(set=index)
@@ -211,10 +212,10 @@ romer <- function(index,y,design,contrast=ncol(design),array.weights=NULL,block=
c(top,bottom)
}
-.romer.mean.floormean <- function(index,y,design,contrast=ncol(design),array.weights=NULL,block=NULL,correlation,floor=FALSE,nrot=9999)
+.romer.mean.floormean <- function(y,index,design,contrast=ncol(design),array.weights=NULL,block=NULL,correlation,floor=FALSE,nrot=9999)
# rotation mean-rank version of GSEA (gene set enrichment analysis) for linear models
# Gordon Smyth and Yifang Hu
-# 27 March 2009. Last modified 5 Oct 2009.
+# 27 March 2009. Last modified 20 Oct 2014.
{
# Check input arguments
if(!is.list(index)) index <- list(set=index)
diff --git a/inst/doc/changelog.txt b/inst/doc/changelog.txt
index 03a2d2d..7de2b0c 100755
--- a/inst/doc/changelog.txt
+++ b/inst/doc/changelog.txt
@@ -1,3 +1,9 @@
+20 Oct 2014: limma 3.22.1
+
+- romer() is now an S3 generic function.
+
+14 Oct 2014: limma 3.22.0 (Bioconductor 3.0 Release Branch)
+
10 Oct 2014: limma 3.21.21
- arrayWeights() with plot=TRUE now resets graphics parameters to
diff --git a/inst/doc/intro.pdf b/inst/doc/intro.pdf
index 1c6a399..c19625c 100644
Binary files a/inst/doc/intro.pdf and b/inst/doc/intro.pdf differ
diff --git a/man/romer.Rd b/man/romer.Rd
index b15171c..4fd5b2c 100644
--- a/man/romer.Rd
+++ b/man/romer.Rd
@@ -1,23 +1,26 @@
\name{romer}
\alias{romer}
+\alias{romer.default}
+
\title{Rotation Gene Set Enrichment Analysis}
\description{
Gene set enrichment analysis for linear models using rotation tests (ROtation testing using MEan Ranks).
}
\usage{
-romer(index, y, design, contrast=ncol(design), array.weights=NULL, block=NULL,
- correlation, set.statistic="mean", nrot=9999)
+\S3method{romer}{default}(y, index, design, contrast=ncol(design), array.weights=NULL,
+ block=NULL, correlation, set.statistic="mean", nrot=9999, \dots)
}
\arguments{
- \item{index}{list of indices specifying the rows of \code{y} in the gene sets. The list can be made using \link{ids2indices}.}
\item{y}{numeric matrix giving log-expression values.}
- \item{design}{design matrix}
+ \item{index}{list of indices specifying the rows of \code{y} in the gene sets. The list can be made using \link{ids2indices}.}
+ \item{design}{design matrix.}
\item{contrast}{contrast for which the test is required. Can be an integer specifying a column of \code{design}, or else a contrast vector of length equal to the number of columns of \code{design}.}
\item{array.weights}{optional numeric vector of array weights.}
\item{block}{optional vector of blocks.}
\item{correlation}{correlation between blocks.}
\item{set.statistic}{statistic used to summarize the gene ranks for each set. Possible values are \code{"mean"}, \code{"floormean"} or \code{"mean50"}.}
\item{nrot}{number of rotations used to estimate the p-values.}
+ \item{\dots}{other arguments not currently used.}
}
\value{
Numeric matrix giving p-values and the number of matched genes in each gene set.
@@ -62,6 +65,7 @@ This statistic performs well in practice but is slightly slower to compute.
\code{\link{topRomer}},
\code{\link{ids2indices}},
\code{\link{roast}},
+\code{\link{camera}},
\code{\link{wilcoxGST}}
There is a topic page on \link{10.GeneSetTests}.
@@ -96,7 +100,7 @@ y[index,3:4] <- y[index,3:4]+3
index1 <- 1:5
index2 <- 6:10
-r <- romer(index=list(set1=index1,set2=index2),y=y,design=design,contrast=2,nrot=99)
+r <- romer(y=y,index=list(set1=index1,set2=index2),design=design,contrast=2,nrot=99)
r
topRomer(r,alt="up")
topRomer(r,alt="down")
diff --git a/tests/limma-Tests.Rout.save b/tests/limma-Tests.Rout.save
index ed546a1..33f6bb2 100755
--- a/tests/limma-Tests.Rout.save
+++ b/tests/limma-Tests.Rout.save
@@ -1267,7 +1267,7 @@ GO:0006959 1 0 0.0625 1
> proc.time()
user system elapsed
5.89 0.21 6.10
- limma/vignettes/ 0000755 0001263 0001264 00000000000 12417066740 015253 5 ustar 00biocbuild phs_compbio [...]
+ limma/vignettes/ 0000755 0001263 0001264 00000000000 12421323653 015245 5 ustar 00biocbuild phs_compbio [...]
%\VignetteDepends{}
%\VignetteKeywords{microarray linear model}
%\VignettePackage{limma}
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