[med-svn] [r-bioc-edger] branch upstream updated (4c03fbb -> 2285a83)
Andreas Tille
tille at debian.org
Fri Jun 27 14:42:40 UTC 2014
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 4c03fbb Imported Upstream version 3.4.2+dfsg
new 2285a83 Imported Upstream version 3.6.2+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 | 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(-)
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
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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