[med-svn] [r-bioc-edger] 02/06: Merge tag 'upstream/3.8.0+dfsg'

[Andreas Tille]

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

commit ba4a5fdf1ef2f0825efab956de43a58d01523b50
Merge: 0c0f49c 0d6d1ce
Author: Andreas Tille <tille at debian.org>
Date:   Thu Oct 16 13:46:27 2014 +0200

    Merge tag 'upstream/3.8.0+dfsg'
    
    Upstream version 3.8.0+dfsg

 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(-)

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