[med-svn] [r-bioc-mergeomics] 03/03: Merge tag 'upstream/1.4.0'

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository r-bioc-mergeomics.

commit e06bf9a75080c650946b89e1ebe4b80eb02d778b
Merge: b2c5b10 34a5e2d
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Mon Jul 24 21:49:06 2017 +0200

    Merge tag 'upstream/1.4.0'
    
    Upstream version 1.4.0

 DESCRIPTION                        |   4 +-
 R/cle.LS.R                         | 498 ++++++++++++++++++++-----------------
 build/vignette.rds                 | Bin 233 -> 231 bytes
 inst/doc/Mergeomics.Rnw            |   8 +-
 inst/doc/Mergeomics.pdf            | Bin 265347 -> 265168 bytes
 inst/unitTests/test_ssea.analyze.R |   4 +-
 man/MSEA.KDA.onestep.Rd            |   8 +-
 man/Mergeomics-package.Rd          |   8 +-
 man/kda.analyze.Rd                 |   8 +-
 man/kda.analyze.exec.Rd            |  16 +-
 man/kda.analyze.simulate.Rd        |  16 +-
 man/kda.analyze.test.Rd            |  16 +-
 man/kda.configure.Rd               |   8 +-
 man/kda.finish.Rd                  |   8 +-
 man/kda.finish.estimate.Rd         |   8 +-
 man/kda.finish.save.Rd             |   8 +-
 man/kda.finish.summarize.Rd        |   8 +-
 man/kda.finish.trim.Rd             |   8 +-
 man/kda.prepare.Rd                 |  16 +-
 man/kda.prepare.overlap.Rd         |   8 +-
 man/kda.prepare.screen.Rd          |   8 +-
 man/kda.start.Rd                   |  16 +-
 man/kda.start.edges.Rd             |   8 +-
 man/kda.start.identify.Rd          |   8 +-
 man/kda.start.modules.Rd           |   8 +-
 man/kda2cytoscape.Rd               |   8 +-
 man/kda2cytoscape.colorize.Rd      |   8 +-
 man/kda2cytoscape.colormap.Rd      |   8 +-
 man/kda2cytoscape.drivers.Rd       |   8 +-
 man/kda2cytoscape.edges.Rd         |   8 +-
 man/kda2cytoscape.exec.Rd          |   8 +-
 man/kda2cytoscape.identify.Rd      |   8 +-
 man/kda2himmeli.Rd                 |   8 +-
 man/kda2himmeli.colorize.Rd        |   8 +-
 man/kda2himmeli.colormap.Rd        |   8 +-
 man/kda2himmeli.drivers.Rd         |   8 +-
 man/kda2himmeli.edges.Rd           |   8 +-
 man/kda2himmeli.exec.Rd            |   8 +-
 man/kda2himmeli.identify.Rd        |   8 +-
 man/ssea.analyze.Rd                |  25 +-
 man/ssea.analyze.observe.Rd        |  10 +-
 man/ssea.analyze.randgenes.Rd      |  51 +++-
 man/ssea.analyze.randloci.Rd       |  10 +-
 man/ssea.analyze.simulate.Rd       |  29 ++-
 man/ssea.analyze.statistic.Rd      |   8 +-
 man/ssea.control.Rd                |  10 +-
 man/ssea.finish.Rd                 |  10 +-
 man/ssea.finish.details.Rd         |  10 +-
 man/ssea.finish.fdr.Rd             |  10 +-
 man/ssea.finish.genes.Rd           |  10 +-
 man/ssea.meta.Rd                   |   8 +-
 man/ssea.prepare.Rd                |  10 +-
 man/ssea.prepare.counts.Rd         |  10 +-
 man/ssea.prepare.structure.Rd      |  10 +-
 man/ssea.start.Rd                  |   8 +-
 man/ssea.start.configure.Rd        |  10 +-
 man/ssea.start.identify.Rd         |   8 +-
 man/ssea.start.relabel.Rd          |  10 +-
 man/ssea2kda.Rd                    |   8 +-
 man/ssea2kda.analyze.Rd            |  10 +-
 man/ssea2kda.import.Rd             |  10 +-
 man/tool.aggregate.Rd              |   8 +-
 man/tool.cluster.Rd                |  10 +-
 man/tool.cluster.static.Rd         |   8 +-
 man/tool.coalesce.Rd               |  10 +-
 man/tool.coalesce.exec.Rd          |   8 +-
 man/tool.coalesce.find.Rd          |   8 +-
 man/tool.coalesce.merge.Rd         |   8 +-
 vignettes/Mergeomics.Rnw           |   8 +-
 69 files changed, 634 insertions(+), 537 deletions(-)

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