[med-svn] [r-bioc-edger] branch upstream updated (10b108d -> b57357d)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository r-bioc-edger.

      from  10b108d   Imported Upstream version 3.8.2+dfsg
       new  b57357d   Imported Upstream version 3.10.2+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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/{camera.DGEList.R => romer.DGEList.R} |   8 +-
 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, 1200 insertions(+), 1024 deletions(-)
 create mode 100644 R/dropEmptyLevels.R
 rename R/{treatDGE.R => glmTreat.R} (59%)
 copy R/{camera.DGEList.R => romer.DGEList.R} (80%)
 create mode 100644 man/dropEmptyLevels.Rd
 rename man/{treatDGE.Rd => glmTreat.Rd} (56%)
 create mode 100644 man/romer.DGEList.Rd
 delete mode 100755 vignettes/edgeR.Rnw

-- 
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