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commit 691b0494663e091bb67bc3962e8767093092f850 Author: Andreas Tille <[email protected]> Date: Thu Sep 18 15:42:16 2014 +0200 Imported Upstream version 3.6.8+dfsg --- DESCRIPTION | 6 +++--- R/readDGE.R | 2 +- inst/doc/edgeR.pdf | Bin 48051 -> 48051 bytes tests/edgeR-Tests.Rout.save | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 800276a..1060425 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: edgeR -Version: 3.6.7 -Date: 2014/07/15 +Version: 3.6.8 +Date: 2014/08/14 Title: Empirical analysis of digital gene expression data in R Author: Yunshun Chen <[email protected]>, Davis McCarthy <[email protected]>, Aaron Lun <[email protected]>, Mark Robinson <[email protected]>, Xiaobei Zhou <[email protected]>, Gordon Smyth <[email protected]> Maintainer: Yunshun Chen <[email protected]>, Mark Robinson <[email protected]>, Davis McCarthy <[email protected]>, Gordon Smyth <[email protected]> @@ -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: 2014-07-16 02:04:59 UTC; biocbuild +Packaged: 2014-08-15 02:04:09 UTC; biocbuild diff --git a/R/readDGE.R b/R/readDGE.R index 5b26cff..67af8c2 100644 --- a/R/readDGE.R +++ b/R/readDGE.R @@ -8,7 +8,7 @@ readDGE <- function(files,path=NULL,columns=c(1,2),group=NULL,labels=NULL,...) if(is.null(labels)) labels <- row.names(files) files <- files$files } else { - x$samples <- data.frame(files=as.character(files),stringsAsFactors=FALSE) + x$samples <- data.frame(files=as.character(files),group=1,stringsAsFactors=FALSE) } if(!is.null(group)) x$samples$group <- group if(!is.null(x$samples$group)) x$samples$group <- as.factor(x$samples$group) diff --git a/inst/doc/edgeR.pdf b/inst/doc/edgeR.pdf index 7c5c896..607b303 100644 Binary files a/inst/doc/edgeR.pdf and b/inst/doc/edgeR.pdf differ diff --git a/tests/edgeR-Tests.Rout.save b/tests/edgeR-Tests.Rout.save index 07a738b..8fc2197 100644 --- a/tests/edgeR-Tests.Rout.save +++ b/tests/edgeR-Tests.Rout.save @@ -422,7 +422,7 @@ $n0 > proc.time() user system elapsed 3.41 0.03 3.44 - edgeR/vignettes/ 0000755 0001263 0001264 00000000000 12361356713 015202 5 [...] + edgeR/vignettes/ 0000755 0001263 0001264 00000000000 12373265231 015177 5 [...] %\VignetteKeyword{RNA-Seq} %\VignetteKeyword{differential expression} %\VignettePackage{edgeR} -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-edger.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
