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commit 4c03fbbf37f4a4a16254cd9f7967b341d847c814 Author: Andreas Tille <[email protected]> Date: Sun Jan 5 00:31:01 2014 +0100 Imported Upstream version 3.4.2+dfsg --- DESCRIPTION | 8 ++++---- R/subsetting.R | 4 ++++ inst/doc/edgeR.pdf | Bin 49354 -> 49354 bytes 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5a6d032..272f2be 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,9 +1,9 @@ Package: edgeR -Version: 3.4.0 +Version: 3.4.2 Date: 2013/08/31 Title: Empirical analysis of digital gene expression data in R -Author: Mark Robinson <[email protected]>, Davis McCarthy <[email protected]>, Yunshun Chen <[email protected]>, Aaron Lun <[email protected]>, Gordon Smyth <[email protected]> -Maintainer: Mark Robinson <[email protected]>, Davis McCarthy +Author: Mark Robinson <[email protected]>, Davis McCarthy <[email protected]>, Yunshun Chen <[email protected]>, Aaron Lun <[email protected]>, Gordon Smyth <[email protected]> +Maintainer: Mark Robinson <[email protected]>, Davis McCarthy <[email protected]>, Yunshun Chen <[email protected]>, Gordon Smyth <[email protected]> Depends: R (>= 2.15.0), methods, limma @@ -12,4 +12,4 @@ biocViews: Bioinformatics, DifferentialExpression, SAGE, HighThroughputSequencing, RNAseq, ChIPseq 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. License: GPL (>=2) -Packaged: 2013-10-15 03:48:20 UTC; biocbuild +Packaged: 2013-12-06 04:48:35 UTC; biocbuild diff --git a/R/subsetting.R b/R/subsetting.R index 8945612..298a020 100644 --- a/R/subsetting.R +++ b/R/subsetting.R @@ -33,6 +33,8 @@ function(object, i, j, ...) { object$genes <- object$genes[i,,drop=FALSE] object$all.zeros <- object$all.zeros[i,drop=FALSE] object$offset <- object$offset[i,,drop=FALSE] + !is.null(object$AveLogCPM) + object$AveLogCPM <- object$AveLogCPM[i,drop=FALSE] } else { object$counts <- object$counts[i,j,drop=FALSE] object$samples <- droplevels(object$samples[j,,drop=FALSE]) @@ -45,6 +47,8 @@ function(object, i, j, ...) { object$genes <- object$genes[i,,drop=FALSE] object$all.zeros <- object$all.zeros[i,drop=FALSE] object$offset <- object$offset[i,,drop=FALSE] + !is.null(object$AveLogCPM) + object$AveLogCPM <- object$AveLogCPM[i,drop=FALSE] } } object diff --git a/inst/doc/edgeR.pdf b/inst/doc/edgeR.pdf index 1e5ab00..93aabfb 100644 Binary files a/inst/doc/edgeR.pdf and b/inst/doc/edgeR.pdf differ -- Alioth's /git/debian-med/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
