[med-svn] [r-bioc-edger] 03/04: Merge tag 'upstream/3.10.3+dfsg'

[Andreas Tille]

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

commit f3be7eb41c3a801e3acf043d01c8006c89930d9c
Merge: 22f107f 76af3f2
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 26 18:34:46 2015 +0200

    Merge tag 'upstream/3.10.3+dfsg'
    
    Upstream version 3.10.3+dfsg

 DESCRIPTION                 |   6 +-
 NAMESPACE                   |  43 +++++----
 R/S3methods.R               |  23 ++++-
 R/adjustedProfileLik.R      |   6 +-
 R/calcNormFactors.R         |  40 ++++----
 R/camera.DGEList.R          |  39 --------
 R/cpm.R                     |   4 +-
 R/diffSpliceDGE.R           |  64 +++++++++----
 R/estimateDisp.R            |   1 +
 R/estimateTrendedDisp.R     |  23 ++---
 R/expandAsMatrix.R          |   7 +-
 R/geneset-DGEList.R         |  80 ++++++++++++++++
 R/glmQLFTest.R              |  11 +--
 R/glmTreat.R                | 135 ++++++++++++++++++---------
 R/glmfit.R                  |  34 ++-----
 R/goana.R                   |  53 ++++++-----
 R/kegga.R                   |  71 ++++++++++++++
 R/mglmLevenberg.R           |   4 +-
 R/mglmOneGroup.R            |   5 +-
 R/mglmOneWay.R              |   3 +-
 R/plotMD.R                  |  48 ++++++++++
 R/readDGE.R                 |  40 +++++---
 R/roast.DGEList.R           |  82 ----------------
 R/romer.DGEList.R           |  39 --------
 R/rpkm.R                    |   4 +-
 R/subsetting.R              |  10 +-
 build/vignette.rds          | Bin 228 -> 229 bytes
 inst/doc/edgeR.pdf          | Bin 48664 -> 48664 bytes
 man/camera.DGEList.Rd       |   2 +-
 man/cpm.Rd                  |   2 +-
 man/diffSpliceDGE.Rd        |   3 +-
 man/dimnames.Rd             |   4 +-
 man/estimateCommonDisp.Rd   |  40 ++++----
 man/expandAsMatrix.Rd       |   3 +-
 man/glmQLFTest.Rd           |   4 +-
 man/glmTreat.Rd             |  14 ++-
 man/glmfit.Rd               |   9 +-
 man/goana.Rd                |  26 +++---
 man/plotMD.Rd               |  77 +++++++++++++++
 man/readDGE.Rd              |  36 +++++---
 man/roast.DGEList.Rd        |   2 +-
 man/romer.DGEList.Rd        |   2 +-
 src/R_levenberg.cpp         |  14 +--
 src/R_one_group.cpp         |  11 ++-
 src/glm.h                   |   6 +-
 src/glm_levenberg.cpp       |  10 +-
 src/glm_one_group.cpp       |   4 +-
 src/matvec_check.cpp        |  22 +----
 src/matvec_check.h          |   2 +-
 tests/edgeR-Tests.Rout.save | 221 ++++++++++++++++++++++++++++++++++----------
 vignettes/edgeR.Rnw         |  48 ++++++++++
 51 files changed, 923 insertions(+), 514 deletions(-)

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