[med-svn] [r-bioc-edger] branch master updated (0c0f49c -> ffbb166)

[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  0c0f49c   New upstream version, reviewed copyright
       new  0d6d1ce   Imported Upstream version 3.8.0+dfsg
       new  ba4a5fd   Merge tag 'upstream/3.8.0+dfsg'
       new  8e33768   New upstream version
       new  3c8f96b   cme fix dpkg-control
       new  acba84b   remove tests requiring locfit from the test suite
       new  ffbb166   Upload to unstable

The 6 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 +++++
 debian/changelog                                |   8 +
 debian/control                                  |   8 +-
 debian/patches/do_not_attempt_locfit_test.patch |  81 ++++
 debian/patches/series                           |   1 +
 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 +-
 67 files changed, 2234 insertions(+), 787 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 debian/patches/do_not_attempt_locfit_test.patch
 create mode 100644 debian/patches/series
 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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