[med-svn] [r-bioc-edger] branch upstream updated (bb9764f -> 3b301b7)

[Andreas Tille]

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

      from  bb9764f   Imported Upstream version 3.14.0+dfsg
       new  3b301b7   Imported Upstream version 3.16.1+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                    |   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(-)
 create mode 100644 R/addPriorCount.R
 create mode 100644 R/makeCompressedMatrix.R
 create mode 100644 man/addPriorCount.Rd
 create mode 100644 man/makeCompressedMatrix.Rd
 create mode 100644 src/R_add_prior_count.cpp
 create mode 100644 src/R_add_repeat_matrices.cpp
 create mode 100644 src/R_ave_log_cpm.cpp
 create mode 100644 src/R_calculate_cpm.cpp
 create mode 100644 src/R_check_counts.cpp
 create mode 100644 src/R_check_poisson_bound.cpp
 create mode 100644 src/R_compute_apl.cpp
 delete mode 100644 src/R_cr_adjust.cpp
 create mode 100644 src/R_get_one_way_fitted.cpp
 create mode 100644 src/R_initialize_levenberg.cpp
 create mode 100644 src/add_prior.cpp
 create mode 100644 src/add_prior.h

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