[med-svn] [r-bioc-edger] branch master updated (8aaa616 -> 2a03d05)

[Andreas Tille]

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

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

      from  8aaa616   Adapt patches
       new  3e2cb85   Use xz option in watch file
       new  bb9764f   Imported Upstream version 3.14.0+dfsg
       new  d3dc869   Merge tag 'upstream/3.14.0+dfsg'
       new  faf8631   New upstream version
       new  425d3d0   cme fix dpkg-control
       new  71f59e7   Refresh patches
       new  2a03d05   Upload to unstable

The 7 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                                     |  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
 debian/changelog                                |   8 +
 debian/control                                  |   4 +-
 debian/patches/do_not_attempt_locfit_test.patch |  20 +-
 debian/rules                                    |   3 -
 debian/watch                                    |   2 +-
 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 +++++++++++++++++-------
 {inst/doc => vignettes}/edgeR.Rnw               |   0
 53 files changed, 960 insertions(+), 506 deletions(-)
 create mode 100644 R/gini.R
 create mode 100644 man/gini.Rd
 copy {inst/doc => vignettes}/edgeR.Rnw (100%)

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