[med-svn] [r-bioc-edger] branch upstream updated (b57357d -> 76af3f2)

[Andreas Tille]

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

      from  b57357d   Imported Upstream version 3.10.2+dfsg
       new  76af3f2   Imported Upstream version 3.10.3+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                       |   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
 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
 51 files changed, 875 insertions(+), 514 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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