[med-svn] [r-bioc-limma] 02/05: Imported Upstream version 3.24.15+dfsg
Andreas Tille
tille at debian.org
Fri Sep 25 20:02:38 UTC 2015
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tille pushed a commit to branch master
in repository r-bioc-limma.
commit 1ef4bdd0ea22d61466a7d0c2d6a25d220538f375
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 25 21:53:43 2015 +0200
Imported Upstream version 3.24.15+dfsg
---
DESCRIPTION | 6 +++---
R/kegga.R | 24 ++++++++++++------------
inst/doc/changelog.txt | 4 ++++
inst/doc/intro.pdf | Bin 46191 -> 46191 bytes
man/goana.Rd | 2 +-
man/topGO.Rd | 9 +++++----
tests/limma-Tests.Rout.save | 14 +++++++++++---
7 files changed, 36 insertions(+), 23 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 17e28c2..306a9fa 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: limma
-Version: 3.24.14
-Date: 2015-07-20
+Version: 3.24.15
+Date: 2015-08-05
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], Aaron Lun [ctb]
@@ -20,4 +20,4 @@ biocViews: ExonArray, GeneExpression, Transcription,
MultipleComparison, Normalization, Preprocessing,
QualityControl
NeedsCompilation: yes
-Packaged: 2015-07-21 01:24:42 UTC; biocbuild
+Packaged: 2015-08-06 01:23:12 UTC; biocbuild
diff --git a/R/kegga.R b/R/kegga.R
index bdfb813..4dd3d76 100644
--- a/R/kegga.R
+++ b/R/kegga.R
@@ -77,7 +77,7 @@ kegga.MArrayLM <- function(de, coef = ncol(de), geneid = rownames(de), FDR = 0.0
kegga.default <- function(de, universe = NULL, species = "Hs", prior.prob = NULL, covariate=NULL, plot=FALSE, ...)
# KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of DE genes
# Gordon Smyth and Yifang Hu
-# Created 18 May 2015. Modified 3 June 2015.
+# Created 18 May 2015. Modified 4 August 2015.
{
# Ensure de is a list
if(!is.list(de)) de <- list(DE = de)
@@ -216,7 +216,7 @@ kegga.default <- function(de, universe = NULL, species = "Hs", prior.prob = NULL
pathname <- KEGGREST::keggList("pathway")
names(pathname) <- gsub("map", organism, names(pathname))
m <- match(g, names(pathname))
- Results <- data.frame(Path = pathname[m], S, P, stringsAsFactors=FALSE)
+ Results <- data.frame(Pathway = pathname[m], S, P, stringsAsFactors=FALSE)
rownames(Results) <- g
# Name p-value columns
@@ -225,10 +225,10 @@ kegga.default <- function(de, universe = NULL, species = "Hs", prior.prob = NULL
Results
}
-topKEGG <- function(results, sort = NULL, number = 20L, truncate.term=NULL)
+topKEGG <- function(results, sort = NULL, number = 20L, truncate.path=NULL)
# Extract top KEGG pathways from kegga output
# Gordon Smyth and Yifang Hu
-# Created 15 May 2015.
+# Created 15 May 2015. Modified 4 August 2015.
{
# Check results
if(!is.data.frame(results)) stop("results should be a data.frame.")
@@ -263,14 +263,14 @@ topKEGG <- function(results, sort = NULL, number = 20L, truncate.term=NULL)
}
tab <- results[o[1L:number],,drop=FALSE]
-# Truncate Term column for readability
- if(!is.null(truncate.term)) {
- truncate.term <- as.integer(truncate.term[1])
- truncate.term <- max(truncate.term,5L)
- truncate.term <- min(truncate.term,1000L)
- tm2 <- truncate.term-3L
- i <- (nchar(tab$Term) > tm2)
- tab$Term[i] <- paste0(substring(tab$Term[i],1L,tm2),"...")
+# Truncate Pathway column for readability
+ if(!is.null(truncate.path)) {
+ truncate.path <- as.integer(truncate.path[1])
+ truncate.path <- max(truncate.path,5L)
+ truncate.path <- min(truncate.path,1000L)
+ tm2 <- truncate.path-3L
+ i <- (nchar(tab$Pathway) > tm2)
+ tab$Pathway[i] <- paste0(substring(tab$Pathway[i],1L,tm2),"...")
}
tab
diff --git a/inst/doc/changelog.txt b/inst/doc/changelog.txt
index 8dcb976..dfd4b2c 100755
--- a/inst/doc/changelog.txt
+++ b/inst/doc/changelog.txt
@@ -1,3 +1,7 @@
+ 5 Aug 2015: limma 3.24.15
+
+- argument truncate.term for topKEGG() renamed to 'truncate.path'.
+
20 July 2015: limma 3.24.14
- camera() has a new argument inter.gene.cor. This allows a preset
diff --git a/inst/doc/intro.pdf b/inst/doc/intro.pdf
index b94678c..65a3286 100644
Binary files a/inst/doc/intro.pdf and b/inst/doc/intro.pdf differ
diff --git a/man/goana.Rd b/man/goana.Rd
index 8466649..4fccbfb 100644
--- a/man/goana.Rd
+++ b/man/goana.Rd
@@ -86,7 +86,7 @@ The \code{goana} method for \code{MArrayLM} objects produces a data frame with a
The row names of the data frame give the GO term IDs.
-The output from \code{kegga} is the same except that row names become KEGG pathway IDs, \code{Term} becomes \code{Path} and there is no \code{Ont} column.
+The output from \code{kegga} is the same except that row names become KEGG pathway IDs, \code{Term} becomes \code{Pathway} and there is no \code{Ont} column.
}
\references{
diff --git a/man/topGO.Rd b/man/topGO.Rd
index 54648c1..2101901 100644
--- a/man/topGO.Rd
+++ b/man/topGO.Rd
@@ -4,21 +4,22 @@
\title{Table of Top GO Terms or Top KEGG Pathways}
\description{
-Extract top GO terms from goana output or top KEGG terms from kegga output.
+Extract top GO terms from goana output or top KEGG pathways from kegga output.
}
\usage{
topGO(results, ontology = c("BP", "CC", "MF"), sort = NULL, number = 20L,
truncate.term = NULL)
-topKEGG(results, sort = NULL, number = 20L, truncate.term = NULL)
+topKEGG(results, sort = NULL, number = 20L, truncate.path = NULL)
}
\arguments{
- \item{results}{data frame produced by \code{\link{goana}}.}
+ \item{results}{data frame produced by \code{\link{goana}} or \code{\link{kegga}}.}
\item{ontology}{character vector of ontologies to be included in output. Elements should be one or more of \code{"BP"}, \code{"CC"} or \code{"MF"}.}
\item{sort}{character vector of names of gene lists for which results are required. Should be one or more of the column names of \code{results}. Defaults to all gene lists.}
- \item{number}{maximum number of top GO terms to list. For all terms, set \code{number=Inf}.}
+ \item{number}{maximum number of top GO terms or top KEGG pathways to list. For all terms or all pathways, set \code{number=Inf}.}
\item{truncate.term}{truncate the name of the GO term at this number of characters.}
+ \item{truncate.path}{truncate the name of the KEGG pathway at this number of characters.}
}
\details{
diff --git a/tests/limma-Tests.Rout.save b/tests/limma-Tests.Rout.save
index f1b47e5..1ac4959 100755
--- a/tests/limma-Tests.Rout.save
+++ b/tests/limma-Tests.Rout.save
@@ -1122,7 +1122,15 @@ attr(,"df1")
attr(,"df2")
[1] Inf
> classifyTestsT(tstat)
-TestRe Median Mean 3rd Qu. Max.
+TestRe.2900320 0.3006936 0.2935101 0.3646949 0.3596385 0.3064203
+ [64] 0.3027439 0.3076483 0.3363356 0.3504336 0.3496698 0.2897618 0.2898810
+ [71] 0.3182290 0.3121707 0.2945001 0.2897549 0.3579410 0.3434376 0.3037970
+ [78] 0.3201893 0.3048412 0.3394079 0.3516034 0.3034589 0.3120384 0.3007827
+ [85] 0.3013925 0.2902524 0.3527793 0.2969359 0.3033756 0.3170187 0.2978833
+ [92] 0.2908437 0.3139422 0.3050183 0.4727609 0.2897104 0.2931671 0.2904177
+ [99] 0.3231607 0.2941699
+> summary(fit$s2.post)
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
0.2518 0.2746 0.3080 0.3425 0.3583 0.7344
>
> y$E[1,1] <- NA
@@ -1252,7 +1260,7 @@ GO:0070062 0.055161144
> proc.time()
user system elapsed
2.83 0.18 3.04
- limma/vignettes/ 0000755 0001263 0001264 00000000000 12553317532 015252 5 ustar 00biocbuild phs_compbio [...]
+ limma/vignettes/ 0000755 0001263 0001264 00000000000 12560533400 015242 5 ustar 00biocbuild phs_compbio [...]
%\VignetteDepends{}
%\VignetteKeywords{microarray linear model}
%\VignettePackage{limma}
@@ -1301,4 +1309,4 @@ and follow the links to the limma package help.
- [...]
\ No newline at end of file
+ [...]
\ No newline at end of file
--
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