[med-svn] [r-bioc-limma] branch upstream updated (c310b4a -> ae68131)
Andreas Tille
tille at debian.org
Thu Oct 16 13:05:06 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-limma.
from c310b4a Imported Upstream version 3.20.9+dfsg
new ae68131 Imported Upstream version 3.22.0+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 | 8 +-
NAMESPACE | 10 ++
R/arrayWeights.R | 384 ++++++++++++++++++++++------------------
R/barcodeplot.R | 382 ++++++++++++++++++++++++++++++++-------
R/diffSplice.R | 121 ++++++++-----
R/geneset-roast.R | 12 +-
R/geneset-romer.R | 8 +-
R/goana.R | 236 ++++++++++++++++++++++++
R/lmfit.R | 3 +-
R/plot.R | 82 ++++-----
R/plotExons.R | 100 +++++++++++
R/plotWithHighlights.R | 91 ++++++++++
R/plotdensities.R | 28 +--
R/plots-ma.R | 243 ++++++++-----------------
R/read-ilmn.R | 20 ++-
R/read-maimages.R | 46 ++---
R/voom.R | 2 +-
R/vooma.R | 77 ++++----
inst/NEWS.Rd | 109 ++++++++++++
inst/doc/changelog.txt | 125 ++++++++++++-
inst/doc/intro.pdf | Bin 46191 -> 46191 bytes
inst/doc/usersguide.pdf | Bin 1017047 -> 0 bytes
man/10GeneSetTests.Rd | 4 +-
man/EList.Rd | 32 ++--
man/TestResults.Rd | 2 +-
man/alias2Symbol.Rd | 3 +
man/anova-method.Rd | 4 +-
man/arrayWeights.Rd | 8 +-
man/asdataframe.Rd | 2 +-
man/backgroundcorrect.Rd | 3 +-
man/barcodeplot.Rd | 87 +++++++--
man/camera.Rd | 8 +-
man/diffSplice.Rd | 24 ++-
man/genas.Rd | 4 +-
man/geneSetTest.Rd | 6 +-
man/gls.series.Rd | 4 +-
man/goana.MArrayLM.Rd | 89 ++++++++++
man/goana.Rd | 77 ++++++++
man/heatdiagram.Rd | 6 +-
man/ids2indices.Rd | 46 +++++
man/imageplot.Rd | 4 +-
man/imageplot3by2.Rd | 4 +-
man/kooperberg.Rd | 2 +-
man/lmFit.Rd | 6 +-
man/loessfit.Rd | 2 +-
man/ma3x3.Rd | 9 +-
man/mdplot.Rd | 15 +-
man/mrlm.Rd | 4 +-
man/nec.Rd | 10 +-
man/normalizeCyclicLoess.Rd | 2 +-
man/normalizeMedianAbsValues.Rd | 2 +-
man/normalizeRobustSpline.Rd | 3 +-
man/normalizeVSN.Rd | 4 +-
man/normalizeWithinArrays.Rd | 2 +-
man/normalizebetweenarrays.Rd | 7 +-
man/normalizeprintorder.Rd | 2 +-
man/normalizequantiles.Rd | 5 +-
man/plot.Rd | 87 +++++----
man/plotDensities.Rd | 20 +--
man/plotExons.Rd | 48 +++++
man/plotFB.Rd | 6 +-
man/plotRLDF.Rd | 4 +-
man/plotSA.Rd | 4 +-
man/plotSplice.Rd | 14 +-
man/plotlines.Rd | 4 +-
man/plotma.Rd | 106 ++++++-----
man/plotma3by2.Rd | 10 +-
man/plotprinttiploess.Rd | 4 +-
man/qqt.Rd | 3 +-
man/qualwt.Rd | 2 +-
man/read.columns.Rd | 6 +-
man/read.idat.Rd | 3 +-
man/read.ilmn.Rd | 2 +-
man/read.ilmn.targets.Rd | 5 +-
man/read.maimages.Rd | 2 +-
man/readGPRHeader.Rd | 7 +-
man/readSpotTypes.Rd | 2 +-
man/readTargets.Rd | 4 +-
man/readgal.Rd | 8 +-
man/removeBatchEffect.Rd | 4 +-
man/roast.Rd | 8 +-
man/romer.Rd | 7 +-
man/selectmodel.Rd | 4 +-
man/strsplit2.Rd | 2 +-
man/summary.Rd | 4 +-
man/symbols2indices.Rd | 28 ---
man/topGO.Rd | 38 ++++
man/topRomer.Rd | 4 +-
man/topSplice.Rd | 20 ++-
man/tricubeMovingAverage.Rd | 12 +-
man/volcanoplot.Rd | 4 +-
man/voom.Rd | 6 +-
man/voomWithQualityWeights.Rd | 73 ++++++++
man/vooma.Rd | 8 +-
man/weightedLowess.Rd | 2 +-
man/writefit.Rd | 2 +-
man/zscore.Rd | 4 +-
tests/limma-Tests.R | 5 +
tests/limma-Tests.Rout.save | 163 +++++++++--------
99 files changed, 2356 insertions(+), 972 deletions(-)
create mode 100644 R/goana.R
create mode 100644 R/plotExons.R
create mode 100644 R/plotWithHighlights.R
delete mode 100644 inst/doc/usersguide.pdf
create mode 100644 man/goana.MArrayLM.Rd
create mode 100644 man/goana.Rd
create mode 100644 man/ids2indices.Rd
create mode 100644 man/plotExons.Rd
delete mode 100644 man/symbols2indices.Rd
create mode 100644 man/topGO.Rd
create mode 100644 man/voomWithQualityWeights.Rd
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