[med-svn] [r-bioc-limma] branch upstream updated (140fe49 -> 1411fa9)
Andreas Tille
tille at debian.org
Fri Jul 31 17:11:27 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository r-bioc-limma.
from 140fe49 Imported Upstream version 3.22.1+dfsg
new 802f308 Imported Upstream version 3.24.13+dfsg
new 3fc04a1 Imported Upstream version 3.24.14+dfsg
new 7a403fe Imported Upstream version 3.24.14+dfsg
new 1411fa9 Imported Upstream version 3.24.14+dfsg
The 4 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 | 18 +-
R/alias2Symbol.R | 28 ++-
R/arrayWeights.R | 7 +-
R/auROC.R | 55 +++++
R/background-normexp.R | 6 +-
R/classes.R | 2 +-
R/dups.R | 8 +-
R/fitFDistRobustly.R | 6 +-
R/genas.R | 19 +-
R/geneset-camera.R | 52 +++--
R/geneset-fry.R | 138 ++++++++++++
R/geneset-ids2indices.R | 14 ++
R/geneset-roast.R | 16 +-
R/geneset-romer.R | 435 +++++++++++++++-----------------------
R/goana.R | 221 +++++++++++--------
R/kegga.R | 277 ++++++++++++++++++++++++
R/lmfit.R | 39 ++--
R/loessFit.R | 10 +-
R/neqc.R | 22 +-
R/norm.R | 24 ++-
R/plot.R | 64 ------
R/plotMD.R | 116 ++++++++++
R/plotMDS.R | 80 ++++---
R/plotWithHighlights.R | 56 ++---
R/plotdensities.R | 40 ++--
R/plots-ma.R | 18 +-
R/predFCm.R | 80 +++----
R/read.idat.R | 24 ++-
R/roc.R | 20 --
R/sepchannel.R | 6 +-
R/squeezeVar.R | 4 +-
R/subsetting.R | 16 +-
R/toptable.R | 3 +-
R/venn.R | 73 +++++--
R/voom.R | 6 +-
R/write.R | 17 +-
build/vignette.rds | Bin 230 -> 231 bytes
inst/CITATION | 25 ++-
inst/NEWS.Rd | 113 ++++++++++
inst/doc/changelog.txt | 315 +++++++++++++++++++++++++--
inst/doc/intro.pdf | Bin 46191 -> 46191 bytes
man/01Introduction.Rd | 20 +-
man/02classes.Rd | 15 ++
man/03reading.Rd | 14 ++
man/04Background.Rd | 15 ++
man/05Normalization.Rd | 15 ++
man/06linearmodels.Rd | 18 ++
man/07SingleChannel.Rd | 15 ++
man/08Tests.Rd | 14 ++
man/09Diagnostics.Rd | 36 +++-
man/10GeneSetTests.Rd | 34 ++-
man/11RNAseq.Rd | 32 ++-
man/EList.Rd | 1 +
man/TestResults.Rd | 5 +-
man/arrayWeights.Rd | 2 +-
man/arrayWeightsQuick.Rd | 2 +-
man/asmalist.Rd | 4 +-
man/auROC.Rd | 14 +-
man/backgroundcorrect.Rd | 4 +-
man/barcodeplot.Rd | 25 ++-
man/camera.Rd | 8 +-
man/decideTests.Rd | 7 +-
man/diffSplice.Rd | 4 +-
man/ebayes.Rd | 8 +-
man/genas.Rd | 10 +
man/getEAWP.Rd | 2 +-
man/goana.MArrayLM.Rd | 89 --------
man/goana.Rd | 111 ++++++++--
man/imageplot.Rd | 2 +-
man/lmFit.Rd | 7 +-
man/malist.Rd | 2 +-
man/mdplot.Rd | 40 ++--
man/modifyWeights.Rd | 2 +-
man/normalizeRobustSpline.Rd | 14 +-
man/normalizeWithinArrays.Rd | 2 +-
man/normalizebetweenarrays.Rd | 2 +-
man/normexpfit.Rd | 6 +-
man/normexpsignal.Rd | 6 +-
man/plot.Rd | 94 --------
man/plotDensities.Rd | 12 +-
man/plotExons.Rd | 2 +-
man/plotMD.Rd | 133 ++++++++++++
man/plotMDS.Rd | 34 +--
man/plotSplice.Rd | 5 +-
man/plotWithHighlights.Rd | 96 +++++++++
man/plotma.Rd | 49 +++--
man/plotma3by2.Rd | 2 +
man/predFCm.Rd | 59 +++---
man/propTrueNull.Rd | 7 +-
man/rankSumTestwithCorrelation.Rd | 5 +-
man/read.idat.Rd | 9 +-
man/read.maimages.Rd | 7 +
man/readGPRHeader.Rd | 8 +-
man/readImaGeneHeader.Rd | 2 +-
man/readgal.Rd | 2 +-
man/rglist.Rd | 2 +-
man/roast.Rd | 31 +--
man/romer.Rd | 34 +--
man/summary.Rd | 2 +-
man/topGO.Rd | 24 ++-
man/topSplice.Rd | 4 +-
man/toptable.Rd | 8 +
man/venn.Rd | 9 +-
man/voom.Rd | 11 +-
man/voomWithQualityWeights.Rd | 34 +--
man/vooma.Rd | 2 +-
src/weighted_lowess.c | 80 ++++---
tests/limma-Tests.R | 13 +-
tests/limma-Tests.Rout.save | 163 +++++++-------
110 files changed, 2757 insertions(+), 1281 deletions(-)
create mode 100755 R/auROC.R
create mode 100644 R/geneset-fry.R
create mode 100644 R/geneset-ids2indices.R
create mode 100644 R/kegga.R
delete mode 100644 R/plot.R
create mode 100644 R/plotMD.R
delete mode 100755 R/roc.R
delete mode 100644 man/goana.MArrayLM.Rd
delete mode 100644 man/plot.Rd
create mode 100644 man/plotMD.Rd
create mode 100644 man/plotWithHighlights.Rd
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