[med-svn] [r-bioc-edger] branch master updated (dc81c7a -> dcbad9f)
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 change to branch master
in repository r-bioc-edger.
from dc81c7a Move debian/upstream to debian/upstream/metadata
new 1a73223 New upstream version, fixed watch file, add get-orig-source target
new 296810d Rather use generic way to remove files via FIles-Excluded
new 2285a83 Imported Upstream version 3.6.2+dfsg
new cb38c96 Merge tag 'upstream/3.6.2+dfsg'
new dcbad9f Add todo item
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 | 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
debian/README.source | 3 -
debian/changelog | 10 +
debian/gbp.conf | 6 -
debian/rules | 3 +
debian/watch | 3 +-
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 +++++++++------------------
110 files changed, 2399 insertions(+), 1483 deletions(-)
create mode 100644 R/estimateGLMRobustDisp.R
delete mode 100644 R/mglmLS.R
delete mode 100644 R/mglmSimple.R
create mode 100644 R/nbinomDeviance.R
create mode 100644 R/processHairpinReads.R
create mode 100644 R/residDF.R
create mode 100644 R/rpkm.R
create mode 100644 R/sumTechReps.R
create mode 100644 R/validDGEList.R
delete mode 100644 debian/README.source
create mode 100644 man/estimateGLMRobustDisp.Rd
create mode 100644 man/nbinomDeviance.Rd
create mode 100644 man/processHairpinReads.Rd
create mode 100644 man/sumTechReps.Rd
create mode 100644 man/validDGEList.Rd
create mode 100644 src/R_compute_nbdev.cpp
create mode 100644 src/R_process_hairpin_reads.c
rename src/{core => }/adj_coxreid.cpp (100%)
rename src/{core => }/fmm_spline.c (100%)
rename src/{core => }/glm.h (69%)
rename src/{core => }/glm_levenberg.cpp (84%)
rename src/{core => }/glm_one_group.cpp (63%)
rename src/{core => }/interpolator.cpp (100%)
rename src/{core => }/interpolator.h (100%)
create mode 100644 src/matvec_check.cpp
create mode 100644 src/matvec_check.h
create mode 100644 src/nbdev.cpp
rename src/{core => }/utils.h (89%)
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