[med-svn] [r-bioc-limma] branch upstream updated (c3b46aa -> fc78793)

[Andreas Tille]

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  c3b46aa   Imported Upstream version 3.18.10~dfsg
       new  fc78793   Imported Upstream version 3.20.7+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                  |  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(-)
 create mode 100644 R/diffSplice.R
 create mode 100644 R/plot.R
 create mode 100644 R/read.idat.R
 create mode 100644 R/tricubeMovingAverage.R
 create mode 100644 R/weightedLowess.R
 create mode 100644 man/10GeneSetTests.Rd
 delete mode 100644 man/10Other.Rd
 create mode 100644 man/11RNAseq.Rd
 create mode 100644 man/diffSplice.Rd
 copy man/{plotma.Rd => plot.Rd} (60%)
 mode change 100755 => 100644
 create mode 100644 man/plotSplice.Rd
 create mode 100644 man/read.idat.Rd
 create mode 100644 man/topSplice.Rd
 create mode 100644 man/tricubeMovingAverage.Rd
 create mode 100644 man/weightedLowess.Rd
 create mode 100644 src/weighted_lowess.c

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