[med-svn] [r-bioc-limma] 04/11: Merge tag 'upstream/3.24.13+dfsg'
Andreas Tille
tille at debian.org
Fri Jul 31 17:11:23 UTC 2015
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tille pushed a commit to branch master
in repository r-bioc-limma.
commit 8e8ae7024aab7a0a47fb98e58e95c33dce707ac9
Merge: 871896f 802f308
Author: Andreas Tille <tille at debian.org>
Date: Sun Jul 19 18:14:11 2015 +0200
Merge tag 'upstream/3.24.13+dfsg'
Upstream version 3.24.13+dfsg
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 | 11 +-
R/geneset-fry.R | 138 ++++++++++++
R/geneset-ids2indices.R | 14 ++
R/geneset-roast.R | 14 +-
R/geneset-romer.R | 435 +++++++++++++++-----------------------
R/goana.R | 221 +++++++++++--------
R/kegga.R | 277 ++++++++++++++++++++++++
R/lmfit.R | 35 +--
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/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 | 297 ++++++++++++++++++++++++--
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/arrayWeights.Rd | 2 +-
man/arrayWeightsQuick.Rd | 2 +-
man/asmalist.Rd | 4 +-
man/auROC.Rd | 14 +-
man/backgroundcorrect.Rd | 4 +-
man/barcodeplot.Rd | 25 ++-
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 | 29 ++-
man/romer.Rd | 34 +--
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 | 229 ++++++++++++--------
vignettes/intro.Rnw | 49 +++++
107 files changed, 2802 insertions(+), 1253 deletions(-)
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