[med-svn] [r-bioc-edger] 03/07: Merge tag 'upstream/3.14.0+dfsg'

[Andreas Tille]

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

commit d3dc86986bd93a824e9d89203347847a322ba1c8
Merge: 3e2cb85 bb9764f
Author: Andreas Tille <tille at debian.org>
Date:   Fri May 20 11:56:14 2016 +0200

    Merge tag 'upstream/3.14.0+dfsg'
    
    Upstream version 3.14.0+dfsg

 DESCRIPTION                       |  10 +-
 NAMESPACE                         |  30 ++++-
 R/DGEList.R                       |  22 ++-
 R/calcNormFactors.R               |   6 +-
 R/cpm.R                           |   5 +-
 R/dispCoxReidInterpolateTagwise.R |   2 +-
 R/equalizeLibSizes.R              |  62 ++++++---
 R/estimateCommonDisp.R            |  75 +++++++----
 R/estimateDisp.R                  | 174 +++++++++++++++---------
 R/estimateGLMCommonDisp.R         |   5 +-
 R/estimateGLMTagwiseDisp.R        |  18 +--
 R/estimateGLMTrendedDisp.R        |  22 +--
 R/estimateTagwiseDisp.R           |  96 ++++++++-----
 R/estimateTrendedDisp.R           |  85 ++++++++----
 R/geneset-DGEList.R               |   9 ++
 R/gini.R                          |  10 ++
 R/glmQLFTest.R                    |  51 ++++---
 R/glmfit.R                        |   2 +
 R/gof.R                           |  46 +------
 R/plotBCV.R                       |  30 +++--
 R/splitIntoGroups.R               |  34 +++--
 R/subsetting.R                    |  10 +-
 build/vignette.rds                | Bin 229 -> 228 bytes
 inst/NEWS.Rd                      |  43 ++++++
 inst/doc/edgeR.pdf                | Bin 45781 -> 48664 bytes
 man/DGEList.Rd                    |   7 +-
 man/WLEB.Rd                       |  17 +--
 man/camera.DGEList.Rd             |   2 +-
 man/diffSpliceDGE.Rd              |   3 +-
 man/equalizeLibSizes.Rd           |  26 ++--
 man/estimateCommonDisp.Rd         |  22 ++-
 man/estimateDisp.Rd               |  45 ++++---
 man/estimateGLMTagwiseDisp.Rd     |   2 +-
 man/estimateGLMTrendedDisp.Rd     |   2 +-
 man/estimateTagwiseDisp.Rd        |  44 +++---
 man/estimateTrendedDisp.Rd        |  22 +--
 man/gini.Rd                       |  31 +++++
 man/glmQLFTest.Rd                 |  10 +-
 man/gof.Rd                        |  24 ++--
 man/movingAverageByCol.Rd         |   1 -
 man/processAmplicons.Rd           |   6 +-
 man/roast.DGEList.Rd              |   6 +-
 man/romer.DGEList.Rd              |   2 +-
 man/splitIntoGroups.Rd            |  27 ++--
 man/zscoreNBinom.Rd               |   2 +-
 tests/edgeR-Tests.R               |   7 +-
 tests/edgeR-Tests.Rout.save       | 274 +++++++++++++++++++++++++++-----------
 vignettes/edgeR.Rnw               |  48 +++++++
 48 files changed, 986 insertions(+), 491 deletions(-)

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