[med-svn] [r-bioc-edger] 04/05: Merge tag 'upstream/3.6.2+dfsg'
Andreas Tille
tille at debian.org
Fri Jun 27 14:42:39 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-edger.
commit cb38c96f2fa12b94c7dd2294c041e98d7eb13d93
Merge: 296810d 2285a83
Author: Andreas Tille <tille at debian.org>
Date: Fri Jun 27 16:38:46 2014 +0200
Merge tag 'upstream/3.6.2+dfsg'
Upstream version 3.6.2+dfsg
DESCRIPTION | 15 +-
NAMESPACE | 4 +-
R/DGEList.R | 3 +
R/adjustedProfileLik.R | 25 +-
R/aveLogCPM.R | 84 ++++--
R/calcNormFactors.R | 14 +-
R/camera.DGEList.R | 25 +-
R/cpm.R | 16 +-
R/dglmStdResid.R | 2 +-
R/dispBinTrend.R | 13 +-
R/dispCoxReid.R | 18 +-
R/dispCoxReidInterpolateTagwise.R | 6 +-
R/estimateCommonDisp.R | 14 +-
R/estimateDisp.R | 19 +-
R/estimateGLMCommonDisp.R | 27 +-
R/estimateGLMRobustDisp.R | 99 ++++++
R/estimateGLMTagwiseDisp.R | 28 +-
R/estimateGLMTrendedDisp.R | 30 +-
R/estimateTagwiseDisp.R | 4 +-
R/exactTest.R | 4 +-
R/exactTestByDeviance.R | 56 +---
R/exactTestBySmallP.R | 8 +-
R/exactTestDoubleTail.R | 2 +-
R/glmQLFTest.R | 11 +-
R/glmfit.R | 107 +++----
R/mglmLS.R | 190 ------------
R/mglmLevenberg.R | 43 +--
R/mglmOneGroup.R | 48 +--
R/mglmOneWay.R | 7 +-
R/mglmSimple.R | 83 -----
R/nbinomDeviance.R | 43 +++
R/plotBCV.R | 2 +-
R/predFC.R | 14 +-
R/processHairpinReads.R | 124 ++++++++
R/residDF.R | 29 ++
R/roast.DGEList.R | 56 ++--
R/rpkm.R | 45 +++
R/subsetting.R | 152 +++-------
R/sumTechReps.R | 44 +++
R/validDGEList.R | 13 +
build/vignette.rds | Bin 227 -> 228 bytes
inst/NEWS.Rd | 97 ++++--
inst/doc/edgeR.Rnw | 5 +-
inst/doc/edgeR.pdf | Bin 49354 -> 48051 bytes
inst/doc/index.html | 2 +-
man/DGELRT-class.Rd | 2 +-
man/adjustedProfileLik.Rd | 3 +-
man/asdataframe.Rd | 2 +-
man/asmatrix.Rd | 2 +-
man/aveLogCPM.Rd | 12 +-
man/calcNormFactors.Rd | 2 +-
man/camera.DGEList.Rd | 47 ++-
man/condLogLikDerSize.Rd | 4 +-
man/cpm.Rd | 18 +-
man/dglmStdResid.Rd | 2 +-
man/dispBinTrend.Rd | 3 +-
man/dispCoxReid.Rd | 14 +-
man/dispCoxReidInterpolateTagwise.Rd | 3 +-
man/estimateDisp.Rd | 4 +-
man/estimateGLMCommonDisp.Rd | 8 +-
man/estimateGLMRobustDisp.Rd | 57 ++++
man/estimateGLMTagwiseDisp.Rd | 10 +-
man/estimateGLMTrendedDisp.Rd | 5 +-
man/estimateTagwiseDisp.Rd | 2 +-
man/estimateTrendedDisp.Rd | 18 +-
man/exactTest.Rd | 4 +-
man/expandAsMatrix.Rd | 3 -
man/glmfit.Rd | 19 +-
man/gof.Rd | 2 +-
man/maPlot.Rd | 2 +-
man/meanvar.Rd | 2 +-
man/mglm.Rd | 62 ++--
man/nbinomDeviance.Rd | 58 ++++
man/normalizeChIPtoInput.Rd | 4 +-
man/plotBCV.Rd | 4 +-
man/plotExonUsage.Rd | 4 +-
man/plotMDS.DGEList.Rd | 4 +-
man/plotSmear.Rd | 2 +-
man/predFC.Rd | 16 +-
man/processHairpinReads.Rd | 55 ++++
man/readDGE.Rd | 4 +-
man/roast.DGEList.Rd | 82 +----
man/subsetting.Rd | 20 +-
man/sumTechReps.Rd | 34 +++
man/topTags.Rd | 1 -
man/validDGEList.Rd | 37 +++
src/Makevars | 12 +-
src/R_compute_nbdev.cpp | 45 +++
src/R_exact_test_by_deviance.cpp | 154 +++-------
src/R_levenberg.cpp | 58 +++-
src/R_one_group.cpp | 38 ++-
src/R_process_hairpin_reads.c | 571 +++++++++++++++++++++++++++++++++++
src/{core => }/adj_coxreid.cpp | 0
src/{core => }/fmm_spline.c | 0
src/{core => }/glm.h | 21 +-
src/{core => }/glm_levenberg.cpp | 66 ++--
src/{core => }/glm_one_group.cpp | 32 +-
src/{core => }/interpolator.cpp | 0
src/{core => }/interpolator.h | 0
src/matvec_check.cpp | 80 +++++
src/matvec_check.h | 19 ++
src/nbdev.cpp | 35 +++
src/{core => }/utils.h | 6 +-
tests/edgeR-Tests.R | 3 +-
tests/edgeR-Tests.Rout.save | 449 +++++++++------------------
105 files changed, 2385 insertions(+), 1472 deletions(-)
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