[med-svn] [r-bioc-limma] branch master updated (1cf2f22 -> 9e8d649)
Andreas Tille
tille at debian.org
Fri Jul 31 17:11:22 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository r-bioc-limma.
from 1cf2f22 New upstream version
new cf3e216 Add repacksuffix
new 871896f New upstream version
new 802f308 Imported Upstream version 3.24.13+dfsg
new 8e8ae70 Merge tag 'upstream/3.24.13+dfsg'
new 3702393 Upload to unstable
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
new a0d92f6 Merge tag 'upstream/3.24.14+dfsg'
new 0ff44a6 New upstream version
new 9e8d649 New upstream version uploaded to unstable
The 11 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
debian/changelog | 12 +
debian/patches/do_not_attempt_GO.db_test.patch | Bin 4605 -> 9604 bytes
debian/patches/do_not_attempt_locfit_test.patch | 12 +-
debian/watch | 2 +-
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 ++++-----
114 files changed, 2776 insertions(+), 1288 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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