[med-svn] [r-bioc-edger] branch master updated (4381887 -> 5af31dc)

[Andreas Tille]

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

      from  4381887   New upstream version
       new  22f107f   Fix watch file
       new  76af3f2   Imported Upstream version 3.10.3+dfsg
       new  f3be7eb   Merge tag 'upstream/3.10.3+dfsg'
       new  5af31dc   New upstream version

The 4 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                       |   6 +-
 NAMESPACE                         |  43 ++++----
 R/S3methods.R                     |  23 +++-
 R/adjustedProfileLik.R            |   6 +-
 R/calcNormFactors.R               |  40 ++++---
 R/camera.DGEList.R                |  39 -------
 R/cpm.R                           |   4 +-
 R/diffSpliceDGE.R                 |  64 +++++++----
 R/estimateDisp.R                  |   1 +
 R/estimateTrendedDisp.R           |  23 ++--
 R/expandAsMatrix.R                |   7 +-
 R/geneset-DGEList.R               |  80 ++++++++++++++
 R/glmQLFTest.R                    |  11 +-
 R/glmTreat.R                      | 135 +++++++++++++++--------
 R/glmfit.R                        |  34 ++----
 R/goana.R                         |  53 ++++-----
 R/kegga.R                         |  71 ++++++++++++
 R/mglmLevenberg.R                 |   4 +-
 R/mglmOneGroup.R                  |   5 +-
 R/mglmOneWay.R                    |   3 +-
 R/plotMD.R                        |  48 +++++++++
 R/readDGE.R                       |  40 ++++---
 R/roast.DGEList.R                 |  82 --------------
 R/romer.DGEList.R                 |  39 -------
 R/rpkm.R                          |   4 +-
 R/subsetting.R                    |  10 +-
 build/vignette.rds                | Bin 228 -> 229 bytes
 debian/changelog                  |   7 ++
 debian/watch                      |   2 +-
 inst/doc/edgeR.pdf                | Bin 48664 -> 48664 bytes
 man/camera.DGEList.Rd             |   2 +-
 man/cpm.Rd                        |   2 +-
 man/diffSpliceDGE.Rd              |   3 +-
 man/dimnames.Rd                   |   4 +-
 man/estimateCommonDisp.Rd         |  40 ++++---
 man/expandAsMatrix.Rd             |   3 +-
 man/glmQLFTest.Rd                 |   4 +-
 man/glmTreat.Rd                   |  14 ++-
 man/glmfit.Rd                     |   9 +-
 man/goana.Rd                      |  26 +++--
 man/plotMD.Rd                     |  77 +++++++++++++
 man/readDGE.Rd                    |  36 ++++---
 man/roast.DGEList.Rd              |   2 +-
 man/romer.DGEList.Rd              |   2 +-
 src/R_levenberg.cpp               |  14 +--
 src/R_one_group.cpp               |  11 +-
 src/glm.h                         |   6 +-
 src/glm_levenberg.cpp             |  10 +-
 src/glm_one_group.cpp             |   4 +-
 src/matvec_check.cpp              |  22 +---
 src/matvec_check.h                |   2 +-
 tests/edgeR-Tests.Rout.save       | 221 +++++++++++++++++++++++++++++---------
 {inst/doc => vignettes}/edgeR.Rnw |   0
 53 files changed, 883 insertions(+), 515 deletions(-)
 delete mode 100644 R/camera.DGEList.R
 create mode 100644 R/geneset-DGEList.R
 create mode 100644 R/kegga.R
 create mode 100644 R/plotMD.R
 delete mode 100644 R/roast.DGEList.R
 delete mode 100644 R/romer.DGEList.R
 create mode 100644 man/plotMD.Rd
 copy {inst/doc => vignettes}/edgeR.Rnw (100%)

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