[med-svn] [r-bioc-limma] branch upstream updated (ff596be -> 5c7fc4d)

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

plessy pushed a change to branch upstream
in repository r-bioc-limma.

      from  ff596be   Imported Upstream version 3.16.18~dfsg
       new  5c7fc4d   Imported Upstream version 3.18.0~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                 |   12 +--
 NAMESPACE                   |    4 +
 R/alias2Symbol.R            |    6 +-
 R/beadCountWeights.R        |   99 +++++++++++++++++
 R/contrastAsCoef.R          |   26 +++++
 R/genas.R                   |  228 +++++++++++++++++++++------------------
 R/geneset-roast.R           |   27 ++---
 R/lmfit.R                   |   98 ++++++++++++-----
 R/loessFit.R                |   50 ++++-----
 R/norm.R                    |    4 +-
 R/plots-ma.R                |  251 ++++++++++++++++++++++++++-----------------
 R/predFCm.R                 |    2 +-
 R/read-ilmn.R               |   36 +++++--
 R/subsetting.R              |    3 +-
 R/toptable.R                |  184 +++++++++++++++++++++----------
 R/treat.R                   |   63 ++++++++---
 build/vignette.rds          |  Bin 0 -> 219 bytes
 inst/doc/changelog.txt      |  180 +++++++++++++++++++++++++++----
 inst/doc/limma.R            |    2 -
 inst/doc/limma.pdf          |  Bin 45597 -> 45597 bytes
 man/01Introduction.Rd       |    3 +-
 man/06linearmodels.Rd       |    3 +-
 man/asmalist.Rd             |    7 ++
 man/beadCountWeights.Rd     |   61 +++++++++++
 man/contrastAsCoef.Rd       |   48 +++++++++
 man/contrasts.fit.Rd        |    2 +-
 man/ebayes.Rd               |   15 ++-
 man/fitfdist.Rd             |    4 +-
 man/genas.Rd                |   88 ++++++++++-----
 man/getEAWP.Rd              |    8 +-
 man/lmFit.Rd                |    3 +
 man/loessfit.Rd             |   86 +++++++++------
 man/plotma.Rd               |    9 +-
 man/predFCm.Rd              |    1 +
 man/propTrueNull.Rd         |    1 +
 man/removeBatchEffect.Rd    |    4 +-
 man/roast.Rd                |    1 +
 man/squeezeVar.Rd           |   23 +++-
 man/targetsA2C.Rd           |    2 +-
 man/toptable.Rd             |   15 ++-
 src/normexp.c               |    4 +-
 tests/limma-Tests.R         |   13 ++-
 tests/limma-Tests.Rout.save |  229 +++++++++++++++++++++++----------------
 43 files changed, 1347 insertions(+), 558 deletions(-)
 create mode 100644 R/beadCountWeights.R
 create mode 100644 R/contrastAsCoef.R
 create mode 100644 build/vignette.rds
 delete mode 100644 inst/doc/limma.R
 create mode 100644 man/beadCountWeights.Rd
 create mode 100644 man/contrastAsCoef.Rd

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.git