[med-svn] [r-bioc-edger] 02/04: Imported Upstream version 3.4.2+dfsg

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-edger.

commit 4c03fbbf37f4a4a16254cd9f7967b341d847c814
Author: Andreas Tille <tille at debian.org>
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 <mrobinson at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Yunshun Chen <yuchen at wehi.edu.au>, Aaron Lun <alun at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>
-Maintainer: Mark Robinson <mrobinson at wehi.edu.au>, Davis McCarthy
+Author: Mark Robinson <mark.robinson at imls.uzh.ch>, Davis McCarthy <dmccarthy at wehi.edu.au>, Yunshun Chen <yuchen at wehi.edu.au>, Aaron Lun <alun at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>
+Maintainer: Mark Robinson <mark.robinson at imls.uzh.ch>, Davis McCarthy
         <dmccarthy at wehi.edu.au>, Yunshun Chen <yuchen at wehi.edu.au>,
         Gordon Smyth <smyth at wehi.edu.au>
 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

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