[med-svn] [r-bioc-edger] branch upstream updated (691b049 -> 0d6d1ce)

[Andreas Tille]

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

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

      from  691b049   Imported Upstream version 3.6.8+dfsg
       new  0d6d1ce   Imported Upstream version 3.8.0+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                       |   8 +-
 NAMESPACE                         |  16 +-
 R/adjustedProfileLik.R            |  17 +-
 R/aveLogCPM.R                     |   5 +-
 R/calcNormFactors.R               |  48 ++--
 R/diffSpliceDGE.R                 | 253 +++++++++++++++++++
 R/equalizeLibSizes.R              |  10 +-
 R/estimateDisp.R                  | 107 ++++----
 R/exactTestByDeviance.R           |   2 +-
 R/glmQLFTest.R                    | 107 ++++----
 R/glmfit.R                        |  12 +-
 R/goana.R                         |  66 +++++
 R/goodTuring.R                    |   2 +-
 R/loessByCol.R                    |   2 +-
 R/maximizeInterpolant.R           |   2 +-
 R/mglmLevenberg.R                 |   2 +-
 R/mglmOneGroup.R                  |  10 +-
 R/mglmOneWay.R                    |  11 +-
 R/nbinomDeviance.R                |   7 +-
 R/processAmplicons.R              | 209 ++++++++++++++++
 R/processHairpinReads.R           | 124 ---------
 R/readDGE.R                       |   4 +-
 R/residDF.R                       |  10 +-
 R/subsetting.R                    |   8 +-
 R/treatDGE.R                      |  96 +++++++
 inst/CITATION                     |  24 +-
 inst/NEWS.Rd                      |  35 ++-
 inst/doc/edgeR.Rnw                |   6 +-
 inst/doc/edgeR.pdf                | Bin 48051 -> 48664 bytes
 man/adjustedProfileLik.Rd         |  14 +-
 man/aveLogCPM.Rd                  |   2 +-
 man/calcNormFactors.Rd            |  15 +-
 man/diffSpliceDGE.Rd              |  71 ++++++
 man/equalizeLibSizes.Rd           |  22 +-
 man/estimateDisp.Rd               |   6 +-
 man/glmQLFTest.Rd                 | 115 +++++++++
 man/glmfit.Rd                     |  36 +--
 man/goana.Rd                      |  67 +++++
 man/mglm.Rd                       |   6 +-
 man/plotQLDisp.Rd                 |  48 ++++
 man/plotSpliceDGE.Rd              |  26 ++
 man/processAmplicons.Rd           |  61 +++++
 man/processHairpinReads.Rd        |  55 ----
 man/topSpliceDGE.Rd               |  33 +++
 man/treatDGE.Rd                   |  62 +++++
 src/Makevars                      |   3 -
 src/R_compute_nbdev.cpp           |  19 +-
 src/R_cr_adjust.cpp               |  21 +-
 src/R_exact_test_by_deviance.cpp  |  25 +-
 src/R_levenberg.cpp               |  53 ++--
 src/R_loess_by_col.cpp            |  24 +-
 src/R_maximize_interpolant.cpp    |  18 +-
 src/R_one_group.cpp               |  56 ++---
 src/R_process_hairpin_reads.c     | 511 +++++++++++++++++++++++++-------------
 src/R_simple_good_turing.cpp      |  24 +-
 src/glm.h                         |   2 +-
 src/glm_one_group.cpp             |  44 ++--
 src/init.cpp                      |  30 +++
 src/matvec_check.cpp              |   4 +-
 src/utils.h                       |  30 ++-
 tests/edgeR-Tests.R               |  14 ++
 tests/edgeR-Tests.Rout.save       | 197 +++++++++++----
 {inst/doc => vignettes}/edgeR.Rnw |   6 +-
 63 files changed, 2140 insertions(+), 783 deletions(-)
 create mode 100644 R/diffSpliceDGE.R
 create mode 100644 R/goana.R
 create mode 100644 R/processAmplicons.R
 delete mode 100644 R/processHairpinReads.R
 create mode 100644 R/treatDGE.R
 create mode 100644 man/diffSpliceDGE.Rd
 create mode 100644 man/glmQLFTest.Rd
 create mode 100644 man/goana.Rd
 create mode 100644 man/plotQLDisp.Rd
 create mode 100644 man/plotSpliceDGE.Rd
 create mode 100644 man/processAmplicons.Rd
 delete mode 100644 man/processHairpinReads.Rd
 create mode 100644 man/topSpliceDGE.Rd
 create mode 100644 man/treatDGE.Rd
 create mode 100644 src/init.cpp
 copy {inst/doc => vignettes}/edgeR.Rnw (93%)

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