[med-svn] [r-bioc-edger] branch master updated (b8261dd -> 4381887)
Andreas Tille
tille at debian.org
Sun Jul 19 21:07:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository r-bioc-edger.
from b8261dd New upstream version
new d02ffe6 Fix watch file
new b57357d Imported Upstream version 3.10.2+dfsg
new 3a44305 Merge tag 'upstream/3.10.2+dfsg'
new 225b55b Adapt patch
new 4381887 New upstream version
The 5 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
debian/changelog | 6 +
debian/patches/do_not_attempt_locfit_test.patch | 23 +-
debian/watch | 2 +-
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 ---
89 files changed, 1208 insertions(+), 1047 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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