[med-svn] [r-bioc-edger] 03/05: Merge tag 'upstream/3.10.2+dfsg'

[Andreas Tille]

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

commit 3a44305a8b1ff54e8913a6c7ddd47638f8ee1eb7
Merge: d02ffe6 b57357d
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jul 19 21:40:04 2015 +0200

    Merge tag 'upstream/3.10.2+dfsg'
    
    Upstream version 3.10.2+dfsg

 DESCRIPTION                          |  13 +-
 NAMESPACE                            |   5 +-
 R/DGEList.R                          |  35 ++-
 R/aveLogCPM.R                        |  13 +-
 R/dispBinTrend.R                     |   4 +-
 R/dispCoxReidSplineTrend.R           |   6 +-
 R/dropEmptyLevels.R                  |  13 +
 R/estimateDisp.R                     |  38 ++-
 R/estimateTrendedDisp.R              |   4 +-
 R/glmQLFTest.R                       |  99 ++++---
 R/{treatDGE.R => glmTreat.R}         |  57 ++--
 R/goana.R                            |   6 +-
 R/locfitByCol.R                      |   8 +-
 R/mglmOneGroup.R                     |   2 +-
 R/plotMDS.DGEList.R                  |  58 ++--
 R/processAmplicons.R                 |  80 ++++--
 R/residDF.R                          |  67 +++--
 R/romer.DGEList.R                    |  39 +++
 R/subsetting.R                       |   4 +-
 R/topTags.R                          |  23 +-
 R/zscoreNBinom.R                     |  24 +-
 build/vignette.rds                   | Bin 229 -> 228 bytes
 inst/CITATION                        |   2 +-
 inst/NEWS.Rd                         |  42 +++
 inst/doc/edgeR.pdf                   | Bin 48664 -> 48664 bytes
 man/DGEExact-class.Rd                |   6 +-
 man/DGEGLM-class.Rd                  |  26 +-
 man/DGELRT-class.Rd                  |  10 +-
 man/DGEList-class.Rd                 |  16 +-
 man/DGEList.Rd                       |   2 +-
 man/asdataframe.Rd                   |   2 +-
 man/aveLogCPM.Rd                     |  11 +-
 man/binomTest.Rd                     |  20 +-
 man/calcNormFactors.Rd               |   4 +-
 man/commonCondLogLikDerDelta.Rd      |   4 +-
 man/condLogLikDerSize.Rd             |   4 +-
 man/cpm.Rd                           |   2 +-
 man/decidetestsDGE.Rd                |   4 +-
 man/dglmStdResid.Rd                  |  16 +-
 man/dim.Rd                           |   6 +-
 man/dispBinTrend.Rd                  |   8 +-
 man/dispCoxReid.Rd                   |   6 +-
 man/dispCoxReidInterpolateTagwise.Rd |  24 +-
 man/dispCoxReidSplineTrend.Rd        |   8 +-
 man/dropEmptyLevels.Rd               |  32 +++
 man/edgeR-package.Rd                 |   3 +
 man/estimateCommonDisp.Rd            |   6 +-
 man/estimateDisp.Rd                  |  12 +-
 man/estimateGLMCommonDisp.Rd         |   6 +-
 man/estimateGLMRobustDisp.Rd         |  12 +-
 man/estimateGLMTagwiseDisp.Rd        |  17 +-
 man/estimateGLMTrendedDisp.Rd        |   9 +-
 man/estimateTagwiseDisp.Rd           |   8 +-
 man/estimateTrendedDisp.Rd           |   4 +-
 man/exactTest.Rd                     |   8 +-
 man/getCounts.Rd                     |   2 +-
 man/getPriorN.Rd                     |   4 +-
 man/glmQLFTest.Rd                    | 129 +++++----
 man/{treatDGE.Rd => glmTreat.Rd}     |  38 ++-
 man/glmfit.Rd                        |  32 +--
 man/gof.Rd                           |  12 +-
 man/goodTuring.Rd                    |   2 +-
 man/maPlot.Rd                        |   6 +-
 man/meanvar.Rd                       |  28 +-
 man/mglm.Rd                          |  12 +-
 man/nbinomDeviance.Rd                |   4 +-
 man/plotBCV.Rd                       |   6 +-
 man/plotMDS.DGEList.Rd               |  45 ++-
 man/plotQLDisp.Rd                    |   4 +-
 man/plotSmear.Rd                     |  14 +-
 man/plotSpliceDGE.Rd                 |   6 +-
 man/predFC.Rd                        |   2 +-
 man/processAmplicons.Rd              |   9 +-
 man/readDGE.Rd                       |   6 +-
 man/roast.DGEList.Rd                 |   2 +-
 man/romer.DGEList.Rd                 |  80 ++++++
 man/splitIntoGroups.Rd               |   2 +-
 man/subsetting.Rd                    |   2 +-
 man/topTags.Rd                       |   9 +-
 man/weightedCondLogLikDerDelta.Rd    |  13 +-
 src/R_one_group.cpp                  |  20 +-
 src/R_process_hairpin_reads.c        | 543 ++++++++++++++++-------------------
 src/init.cpp                         |   4 +-
 src/utils.h                          |  12 +-
 tests/edgeR-Tests.Rout.save          | 221 ++++----------
 vignettes/edgeR.Rnw                  |  48 ----
 86 files changed, 1235 insertions(+), 1020 deletions(-)

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