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commit 3a44305a8b1ff54e8913a6c7ddd47638f8ee1eb7 Merge: d02ffe6 b57357d Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/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
