[med-svn] [r-bioc-limma] 02/03: Merge tag 'upstream/3.28.10+dfsg'

[Gordon Ball]

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

commit 1cd47356b3f9e5ad8feb74e065f6cabb11ff993f
Merge: 00175e1 decb5cf
Author: Gordon Ball <gordon at chronitis.net>
Date:   Tue Jun 21 15:17:16 2016 +0200

    Merge tag 'upstream/3.28.10+dfsg'
    
    Upstream version 3.28.10+dfsg

 DESCRIPTION                    |  17 +-
 NAMESPACE                      |   4 +-
 R/alias2Symbol.R               | 100 +++++--
 R/detectionPValues.R           |  41 +++
 R/diffSplice.R                 |  15 +-
 R/dups.R                       |   2 +-
 R/ebayes.R                     |  48 ++--
 R/{squeezeVar.R => fitFDist.R} |  59 +---
 R/fitFDistRobustly.R           |  66 +++--
 R/fitmixture.R                 |  48 ++++
 R/geneset-camera.R             |  11 +-
 R/geneset-fry.R                | 232 ++++++++-------
 R/geneset-roast.R              | 633 ++++++++++++++++++-----------------------
 R/geneset-romer.R              |  15 +-
 R/goana.R                      |  50 +++-
 R/kegga.R                      | 211 +++++++++-----
 R/lmEffects.R                  | 139 +++++++++
 R/lmfit.R                      |  39 ++-
 R/loessFit.R                   |   2 +-
 R/neqc.R                       |   4 +-
 R/norm.R                       |   7 +-
 R/plotrldf.R                   | 133 +++++++--
 R/propTrueNull.R               |   6 +-
 R/read-maimages.R              |   1 +
 R/read.R                       |  14 +-
 R/read.idat.R                  | 127 ++++++---
 R/sepchannel.R                 |   2 +-
 R/squeezeVar.R                 | 203 +++----------
 R/tricubeMovingAverage.R       |  15 +-
 R/voom.R                       |  15 +-
 build/vignette.rds             | Bin 230 -> 229 bytes
 inst/NEWS.Rd                   | 225 +++++++++++++++
 inst/doc/changelog.txt         | 234 ++++++++++++++-
 inst/doc/intro.pdf             | Bin 46191 -> 46191 bytes
 man/03reading.Rd               |   1 +
 man/10GeneSetTests.Rd          |   2 +-
 man/alias2Symbol.Rd            |  14 +-
 man/camera.Rd                  |  40 ++-
 man/detectionPValue.Rd         |  58 ++++
 man/dupcor.Rd                  |  40 ++-
 man/ebayes.Rd                  |  14 +-
 man/fitfdist.Rd                |  28 +-
 man/fitmixture.Rd              |  66 +++++
 man/fitted.MArrayLM.Rd         |   5 +-
 man/getEAWP.Rd                 |  25 +-
 man/gls.series.Rd              |   4 +-
 man/goana.Rd                   |  53 +++-
 man/ids2indices.Rd             |   6 +-
 man/lmFit.Rd                   |   2 +-
 man/logcosh.Rd                 |  26 ++
 man/marraylm.Rd                |   1 +
 man/nec.Rd                     |   1 +
 man/plotRLDF.Rd                |  70 +++--
 man/propexpr.Rd                |  44 ++-
 man/read.idat.Rd               |  77 +++--
 man/read.maimages.Rd           |   3 +-
 man/removeext.Rd               |  13 +-
 man/roast.Rd                   |  63 ++--
 man/romer.Rd                   |   5 +-
 man/squeezeVar.Rd              |  10 +-
 man/targetsA2C.Rd              |   6 +
 man/venn.Rd                    |  22 +-
 man/voom.Rd                    |  12 +-
 tests/limma-Tests.R            |   4 +
 tests/limma-Tests.Rout.save    |  81 ++++--
 65 files changed, 2326 insertions(+), 1188 deletions(-)

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