[med-svn] [r-bioc-deseq2] 04/05: Merge tag 'upstream/1.12.3'

[Michael Crusoe]

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

misterc-guest pushed a commit to branch master
in repository r-bioc-deseq2.

commit 6cc3860ab49257171ea1e5c65ff1e8711cd01766
Merge: 5cb1f88 16b20a8
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Mon Jun 27 13:42:26 2016 -0700

    Merge tag 'upstream/1.12.3'
    
    Upstream version 1.12.3

 DESCRIPTION                               |  15 +-
 NAMESPACE                                 |  37 ++-
 NEWS                                      |  51 ++-
 R/AllClasses.R                            |  89 ++++--
 R/core.R                                  |  40 ++-
 R/helper.R                                | 169 ++--------
 R/methods.R                               |  56 ++--
 R/plots.R                                 |  11 +-
 R/results.R                               | 217 +++++++------
 R/vst.R                                   |  89 +++++-
 build/vignette.rds                        | Bin 228 -> 229 bytes
 inst/doc/DESeq2.R                         | 496 ++++++++++++++++++++++++++++++
 inst/doc/DESeq2.Rnw                       | 372 ++++++++++++++++++++--
 inst/doc/DESeq2.pdf                       | Bin 642417 -> 700965 bytes
 inst/script/deseq2.R                      | 322 -------------------
 inst/script/runScripts.R                  |  37 ++-
 inst/script/simulateCluster.R             |   5 +-
 inst/script/simulateDE.R                  |  18 +-
 inst/script/simulateLFCAccuracy.R         |   5 +-
 inst/script/simulateOutliers.R            |   5 +-
 inst/script/simulation.Rmd                |  11 +-
 inst/script/simulation.pdf                | Bin 377985 -> 394022 bytes
 {vignettes => inst/script}/vst.nb         |   0
 {vignettes => inst/script}/vst.pdf        | Bin
 man/DESeq.Rd                              |   2 +-
 man/DESeq2-package.Rd                     |   2 +-
 man/DESeqDataSet.Rd                       |  17 +-
 man/estimateSizeFactors.Rd                |  19 +-
 man/fpkm.Rd                               |   9 +-
 man/fpm.Rd                                |   3 +-
 man/nbinomWaldTest.Rd                     |   3 +-
 man/normalizeGeneLength.Rd                |  96 +-----
 man/plotMA.Rd                             |  17 +-
 man/results.Rd                            |  67 ++--
 man/vst.Rd                                |  43 +++
 src/DESeq2.cpp                            |  16 +-
 tests/testthat/test_construction_errors.R |   1 +
 tests/testthat/test_counts_input.R        |   3 +-
 tests/testthat/test_custom_filt.R         |  22 +-
 tests/testthat/test_edge_case.R           |   2 +-
 tests/testthat/test_gene_length.R         |  29 --
 tests/testthat/test_model_matrix.R        |  10 +
 tests/testthat/test_nbinomWald.R          |   7 +
 tests/testthat/test_optim.R               |   6 +-
 tests/testthat/test_outlier.R             |   6 +
 tests/testthat/test_results.R             |   2 +-
 tests/testthat/test_rlog.R                |   2 +
 tests/testthat/test_size_factor.R         |   1 +
 tests/testthat/test_tximport.R            |  22 ++
 tests/testthat/test_vst.R                 |  15 +-
 vignettes/DESeq2.Rnw                      | 372 ++++++++++++++++++++--
 vignettes/library.bib                     |  73 +++++
 52 files changed, 2010 insertions(+), 902 deletions(-)

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