[med-svn] [r-bioc-limma] 03/04: Merge tag 'upstream/3.20.7+dfsg'

[Andreas Tille]

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

commit aefefa50c8592eff537fa80fd3b3a13921eefe20
Merge: a2a7358 fc78793
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 27 19:01:15 2014 +0200

    Merge tag 'upstream/3.20.7+dfsg'
    
    Upstream version 3.20.7+dfsg

 DESCRIPTION                  |  25 ++--
 NAMESPACE                    |  12 +-
 R/barcodeplot.R              | 183 ++++++++++++++++++------
 R/beadCountWeights.R         |  28 ++--
 R/diffSplice.R               | 210 ++++++++++++++++++++++++++++
 R/dups.R                     |   7 +-
 R/fitFDistRobustly.R         |  13 +-
 R/geneset-camera.R           |  53 ++++---
 R/geneset-roast.R            | 325 +++++++++++++++++++++++--------------------
 R/geneset-romer.R            |  24 ++--
 R/lmfit.R                    |   6 +-
 R/loessFit.R                 | 106 ++++++++++----
 R/plot.R                     |  70 ++++++++++
 R/plotMDS.R                  |  53 ++++---
 R/plots-ma.R                 |  28 +++-
 R/read-ilmn.R                |  10 +-
 R/read.idat.R                |  41 ++++++
 R/removeBatchEffect.R        |  16 +--
 R/subsetting.R               |   6 +-
 R/toptable.R                 |  31 +++--
 R/treat.R                    |  16 ++-
 R/tricubeMovingAverage.R     |  18 +++
 R/utility.R                  |   6 +-
 R/weightedLowess.R           |  49 +++++++
 R/zscore.R                   |  25 +++-
 build/vignette.rds           | Bin 229 -> 230 bytes
 inst/NEWS.Rd                 | 117 ++++++++++++++++
 inst/doc/changelog.txt       | 251 ++++++++++++++++++++++++++++++---
 inst/doc/intro.pdf           | Bin 46191 -> 46191 bytes
 man/01Introduction.Rd        |  30 +++-
 man/02classes.Rd             |   2 +-
 man/03reading.Rd             |   4 +-
 man/04Background.Rd          |   2 +-
 man/05Normalization.Rd       |   2 +-
 man/06linearmodels.Rd        |   2 +-
 man/07SingleChannel.Rd       |   2 +-
 man/08Tests.Rd               |   2 +-
 man/09Diagnostics.Rd         |   4 +-
 man/10GeneSetTests.Rd        |  36 +++++
 man/10Other.Rd               |  10 --
 man/11RNAseq.Rd              |  31 +++++
 man/EList.Rd                 |  25 ++--
 man/PrintLayout.Rd           |   9 +-
 man/alias2Symbol.Rd          |   7 +-
 man/arrayWeights.Rd          |  11 +-
 man/arrayWeightsQuick.Rd     |   6 +-
 man/asMatrixWeights.Rd       |   1 -
 man/avearrays.Rd             |   3 +-
 man/barcodeplot.Rd           |  17 ++-
 man/beadCountWeights.Rd      |   8 +-
 man/blockDiag.Rd             |  12 +-
 man/camera.Rd                |  22 +--
 man/changelog.Rd             |   4 +
 man/classifytests.Rd         |   2 +
 man/controlStatus.Rd         |  12 +-
 man/diffSplice.Rd            |  41 ++++++
 man/ebayes.Rd                |   6 +-
 man/genas.Rd                 |   2 +-
 man/geneSetTest.Rd           |   7 +-
 man/heatdiagram.Rd           |   8 +-
 man/imageplot3by2.Rd         |   3 +-
 man/kooperberg.Rd            |   6 +-
 man/lmFit.Rd                 |  14 +-
 man/loessfit.Rd              |  37 +++--
 man/nec.Rd                   |  10 +-
 man/normalizeWithinArrays.Rd |   4 +-
 man/normalizeprintorder.Rd   |   9 +-
 man/{plotma.Rd => plot.Rd}   |  55 +++++---
 man/plotMDS.Rd               |  17 ++-
 man/plotSA.Rd                |   3 +-
 man/plotSplice.Rd            |  29 ++++
 man/plotma.Rd                |  13 +-
 man/plotma3by2.Rd            |   5 +-
 man/poolvar.Rd               |   6 -
 man/printtipWeights.Rd       |  34 +++--
 man/qqt.Rd                   |   6 +-
 man/read.columns.Rd          |   4 +-
 man/read.idat.Rd             |  70 ++++++++++
 man/read.ilmn.Rd             |  27 ++--
 man/read.ilmn.targets.Rd     |   2 +-
 man/read.maimages.Rd         |   5 +-
 man/readGPRHeader.Rd         |  12 +-
 man/removeBatchEffect.Rd     |  19 ++-
 man/roast.Rd                 |  24 ++--
 man/romer.Rd                 |   8 +-
 man/symbols2indices.Rd       |   2 +
 man/targetsA2C.Rd            |   5 +-
 man/topRomer.Rd              |   7 +-
 man/topSplice.Rd             |  34 +++++
 man/toptable.Rd              |  13 +-
 man/tricubeMovingAverage.Rd  |  36 +++++
 man/volcanoplot.Rd           |   4 +-
 man/voom.Rd                  |   7 +-
 man/vooma.Rd                 |   3 +-
 man/weightedLowess.Rd        |  72 ++++++++++
 man/writefit.Rd              |   3 +-
 man/zscore.Rd                |  40 ++++--
 src/weighted_lowess.c        | 271 ++++++++++++++++++++++++++++++++++++
 tests/limma-Tests.R          |  17 ++-
 tests/limma-Tests.Rout.save  | 139 ++++++++++--------
 100 files changed, 2434 insertions(+), 700 deletions(-)

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