[med-svn] [r-bioc-edger] 02/07: Merge tag 'upstream/3.16.1+dfsg'

[Andreas Tille]

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

commit 6ba82adb32e508afaf2f11b0725646e9a1254c33
Merge: 2a03d05 3b301b7
Author: Andreas Tille <tille at debian.org>
Date:   Fri Oct 28 09:49:27 2016 +0200

    Merge tag 'upstream/3.16.1+dfsg'
    
    Upstream version 3.16.1+dfsg

 DESCRIPTION                    |   10 +-
 NAMESPACE                      |    3 +-
 R/DGEList.R                    |   15 +-
 R/addPriorCount.R              |   27 +
 R/adjustedProfileLik.R         |   68 +--
 R/aveLogCPM.R                  |   60 +--
 R/cpm.R                        |   25 +-
 R/diffSpliceDGE.R              |    5 +-
 R/estimateDisp.R               |   82 ++-
 R/expandAsMatrix.R             |   18 +-
 R/glmQLFTest.R                 |   61 +--
 R/glmTreat.R                   |  131 +++--
 R/glmfit.R                     |   15 +-
 R/locfitByCol.R                |    5 +-
 R/makeCompressedMatrix.R       |  164 ++++++
 R/mglmLevenberg.R              |   60 +--
 R/mglmOneGroup.R               |   36 +-
 R/mglmOneWay.R                 |   29 +-
 R/nbinomDeviance.R             |   50 +-
 R/plotMD.R                     |   13 +-
 R/predFC.R                     |   34 +-
 R/readDGE.R                    |   18 +-
 R/spliceVariants.R             |   10 +-
 build/vignette.rds             |  Bin 228 -> 229 bytes
 inst/CITATION                  |   37 +-
 inst/NEWS.Rd                   |   39 ++
 inst/doc/edgeR.pdf             |  Bin 48664 -> 45765 bytes
 man/addPriorCount.Rd           |   52 ++
 man/aveLogCPM.Rd               |    4 +-
 man/edgeR-package.Rd           |   25 +-
 man/estimateDisp.Rd            |    5 +-
 man/expandAsMatrix.Rd          |   21 +-
 man/glmQLFTest.Rd              |   21 +-
 man/glmTreat.Rd                |   20 +-
 man/goodTuring.Rd              |    6 +-
 man/makeCompressedMatrix.Rd    |  108 ++++
 man/plotMD.Rd                  |    3 +
 man/plotQLDisp.Rd              |   11 +-
 man/plotSmear.Rd               |   17 +-
 man/predFC.Rd                  |    7 +-
 man/processAmplicons.Rd        |   34 +-
 src/R_add_prior_count.cpp      |   64 +++
 src/R_add_repeat_matrices.cpp  |   41 ++
 src/R_ave_log_cpm.cpp          |   62 +++
 src/R_calculate_cpm.cpp        |   86 ++++
 src/R_check_counts.cpp         |  137 +++++
 src/R_check_poisson_bound.cpp  |   50 ++
 src/R_compute_apl.cpp          |  111 +++++
 src/R_compute_nbdev.cpp        |  113 +++--
 src/R_cr_adjust.cpp            |   43 --
 src/R_get_one_way_fitted.cpp   |   60 +++
 src/R_initialize_levenberg.cpp |  206 ++++++++
 src/R_levenberg.cpp            |  105 ++--
 src/R_one_group.cpp            |  136 +++--
 src/add_prior.cpp              |   56 +++
 src/add_prior.h                |   25 +
 src/adj_coxreid.cpp            |   62 ++-
 src/glm.h                      |   17 +-
 src/glm_levenberg.cpp          |  120 ++---
 src/glm_one_group.cpp          |   20 +-
 src/init.cpp                   |   24 +-
 src/matvec_check.cpp           |  178 +++++--
 src/matvec_check.h             |   32 +-
 src/nbdev.cpp                  |    2 +-
 src/utils.h                    |   42 +-
 tests/edgeR-Tests.Rout.save    | 1079 ++++++++++++++++++++--------------------
 66 files changed, 2836 insertions(+), 1384 deletions(-)

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