[med-svn] [r-bioc-mergeomics] branch upstream updated (d1f6047 -> 34a5e2d)

[Dylan Aïssi]

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bob.dybian-guest pushed a change to branch upstream
in repository r-bioc-mergeomics.

      from  d1f6047   Imported Upstream version 1.2.0
       new  34a5e2d   Imported Upstream version 1.4.0

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                        |   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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