[med-svn] [r-bioc-limma] 02/08: Merge tag 'upstream/3.22.0+dfsg'

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository r-bioc-limma.

commit 579a4f235864d047519ea4219f10f521172591ca
Merge: c30f250 ae68131
Author: Andreas Tille <tille at debian.org>
Date:   Thu Oct 16 13:38:55 2014 +0200

    Merge tag 'upstream/3.22.0+dfsg'
    
    Upstream version 3.22.0+dfsg

 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(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.git