SVN: Bioconductor (trunk)

Revision 76868 by khansen

khansen — Fri, 24 May 2013 00:00:00 GMT

changed license to EPL, as per discussion amongst authors

(Fri, 24 May 2013 00:00:00 GMT)

Deleted	/trunk/madman/Rpacks/Rgraphviz/LICENSE
Modified	/trunk/madman/Rpacks/Rgraphviz/DESCRIPTION

Revision 76867 by r.day

r.day — Fri, 24 May 2013 14:27:50 GMT

Exported logTen and logTen.DataFilter

(Fri, 24 May 2013 14:27:50 GMT)

Modified

/trunk/madman/Rpacks/IdMappingAnalysis/NAMESPACE

Revision 76866 by khansen

khansen — Fri, 24 May 2013 14:26:29 GMT

Updates to the GenomicMethylSet and GenomicRatioSet constructors required by a change in GenomicRanges, reported by Gustavo Fernandez Bayon 

                (Fri, 24 May 2013 14:26:29 GMT)


                
        Modified
	 /trunk/madman/Rpacks/minfi/inst/NEWS.Rd
Modified
	 /trunk/madman/Rpacks/minfi/man/GenomicRatioSet-class.Rd
Modified
	 /trunk/madman/Rpacks/minfi/R/gmset.R
Modified
	 /trunk/madman/Rpacks/minfi/man/GenomicMethylSet-class.Rd
Modified
	 /trunk/madman/Rpacks/minfi/DESCRIPTION
Modified
	 /trunk/madman/Rpacks/minfi/R/grset.R

Revision 76865 by r.day

r.day — Fri, 24 May 2013 13:28:25 GMT

Removing duplicate, IdMappingAnalysis-dash-package.Rd

(Fri, 24 May 2013 13:28:25 GMT)

Deleted

/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMappingAnalysis-dash-package.Rd

Revision 76864 by a.reyes

a.reyes — Fri, 24 May 2013 12:08:30 GMT

fixed problem with complex formulas and genes with two exons

(Fri, 24 May 2013 12:08:30 GMT)

Modified	/trunk/madman/Rpacks/DEXSeq/NAMESPACE
Modified	/trunk/madman/Rpacks/DEXSeq/man/ExonCountSet-class.Rd
Modified	/trunk/madman/Rpacks/DEXSeq/R/core_functions.R
Modified	/trunk/madman/Rpacks/DEXSeq/DESCRIPTION

Revision 76861 by t.yin

t.yin — Fri, 24 May 2013 02:57:01 GMT

fix rect to circle smooth bugs

(Fri, 24 May 2013 02:57:01 GMT)

Modified

/trunk/madman/Rpacks/biovizBase/R/transform.R

Revision 76860 by r.day

r.day — Fri, 24 May 2013 02:12:57 GMT

in DataFilter.Rd,
inserted a missing "}",
and removed the "..." argument.

(Fri, 24 May 2013 02:12:57 GMT)

Modified

/trunk/madman/Rpacks/IdMappingAnalysis/man/DataFilter.Rd

Revision 76859 by r.day

r.day — Fri, 24 May 2013 02:11:55 GMT

Corrected spelling "encapsultate..." in a few files.

(Fri, 24 May 2013 02:11:55 GMT)

Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getCorrDataFrame.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMapDiff.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/Bootstrap.Rd

Revision 76858 by radivot

radivot — Fri, 24 May 2013 01:15:10 GMT

changed name of class of objects to SBMLR to avoid collisions with SBML objects of rsbml.
Similarly, I also changed simulate to sim and updated the examples to reflect this.

(Fri, 24 May 2013 01:15:10 GMT)

Modified	/trunk/madman/Rpacks/SBMLR/inst/doc/quick-start.Rnw
Modified	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/Fig5RossYeoh.r
Deleted	/trunk/madman/Rpacks/SBMLR/R/Ops.SBML.r
Added	/trunk/madman/Rpacks/SBMLR/man/sim.Rd
Modified	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/Fig3ross.r
Deleted	/trunk/madman/Rpacks/SBMLR/inst/doc/manual.pdf
Deleted	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/BMCcancerFolates.pdf
Deleted	/trunk/madman/Rpacks/SBMLR/man/Ops.SBML.Rd
Modified	/trunk/madman/Rpacks/SBMLR/man/saveSBMLR.Rd
Modified	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/preFig6Rand.r
Added	/trunk/madman/Rpacks/SBMLR/R/Ops.SBMLR.r
Added	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/readme.txt
Deleted	/trunk/madman/Rpacks/SBMLR/R/simulate.r
Modified	/trunk/madman/Rpacks/SBMLR/inst/models/sbmlrDemo.R
Modified	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/Fig4yeoh.r
Modified	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/Fig7cheungData.r
Added	/trunk/madman/Rpacks/SBMLR/R/sim.r
Modified	/trunk/madman/Rpacks/SBMLR/R/readSBML.r
Deleted	/trunk/madman/Rpacks/SBMLR/R/summary.SBML.r
Modified	/trunk/madman/Rpacks/SBMLR/man/saveSBML.Rd
Modified	/trunk/madman/Rpacks/SBMLR/NAMESPACE
Added	/trunk/madman/Rpacks/SBMLR/man/Ops.SBMLR.Rd
Modified	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/Fig8cheung.r
Deleted	/trunk/madman/Rpacks/SBMLR/man/simulate.Rd
Modified	/trunk/madman/Rpacks/SBMLR/inst/doc/manual.doc
Modified	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/Fig2runMorrisonAllegra.r
Deleted	/trunk/madman/Rpacks/SBMLR/inst/doc/BMC.BioInformatics04.pdf
Deleted	/trunk/madman/Rpacks/SBMLR/man/summary.SBML.Rd
Modified	/trunk/madman/Rpacks/SBMLR/inst/BMCcancerFolates/Fig6Rand.r
Modified	/trunk/madman/Rpacks/SBMLR/man/readSBML.Rd
Modified	/trunk/madman/Rpacks/SBMLR/R/readSBMLR.r
Modified	/trunk/madman/Rpacks/SBMLR/NEWS
Added	/trunk/madman/Rpacks/SBMLR/R/summary.SBMLR.r
Modified	/trunk/madman/Rpacks/SBMLR/DESCRIPTION
Modified	/trunk/madman/Rpacks/SBMLR/man/readSBMLR.Rd
Added	/trunk/madman/Rpacks/SBMLR/man/summary.SBMLR.Rd

Revision 76856 by y.liao

y.liao — Thu, 23 May 2013 23:40:28 GMT

(1) copyright header added; (2) new codes copied from subread-1.3.3-p3

(Thu, 23 May 2013 23:40:28 GMT)

Modified

/trunk/madman/Rpacks/Rsubread/src/readSummary.c

Revision 76855 by y.liao

y.liao — Thu, 23 May 2013 23:36:03 GMT

(1) copyright header added; (2) new codes copied from subread-1.3.3-p3

(Thu, 23 May 2013 23:36:03 GMT)

Modified

/trunk/madman/Rpacks/Rsubread/src/readSummary.c

Revision 76854 by y.liao

y.liao — Thu, 23 May 2013 23:35:25 GMT

(1) copyright header added; (2) new codes copied from subread-1.3.3-p3

(Thu, 23 May 2013 23:35:25 GMT)

Modified	/trunk/madman/Rpacks/Rsubread/src/input-files.c
Modified	/trunk/madman/Rpacks/Rsubread/src/SNPCalling.h
Modified	/trunk/madman/Rpacks/Rsubread/src/R_wrapper.c
Modified	/trunk/madman/Rpacks/Rsubread/src/exon-align.c
Modified	/trunk/madman/Rpacks/Rsubread/src/gene-value-index.h
Modified	/trunk/madman/Rpacks/Rsubread/src/input-files.h
Modified	/trunk/madman/Rpacks/Rsubread/src/qualityScores.c
Modified	/trunk/madman/Rpacks/Rsubread/src/atgcContent.c
Modified	/trunk/madman/Rpacks/Rsubread/src/detectionCall.c
Modified	/trunk/madman/Rpacks/Rsubread/src/sambam-file.c
Modified	/trunk/madman/Rpacks/Rsubread/src/exon-algorithms.c
Modified	/trunk/madman/Rpacks/Rsubread/src/sambam-file.h
Modified	/trunk/madman/Rpacks/Rsubread/src/exon-algorithms.h
Modified	/trunk/madman/Rpacks/Rsubread/src/sorted-hashtable.c
Modified	/trunk/madman/Rpacks/Rsubread/src/sorted-hashtable.h
Modified	/trunk/madman/Rpacks/Rsubread/src/detectionCallAnnotation.c
Modified	/trunk/madman/Rpacks/Rsubread/src/propmapped.c
Modified	/trunk/madman/Rpacks/Rsubread/src/fullscan.c
Modified	/trunk/madman/Rpacks/Rsubread/src/HelperFunctions.c
Modified	/trunk/madman/Rpacks/Rsubread/src/sam2bed.c
Modified	/trunk/madman/Rpacks/Rsubread/src/HelperFunctions.h
Modified	/trunk/madman/Rpacks/Rsubread/src/aligner.c
Modified	/trunk/madman/Rpacks/Rsubread/src/removeDupReads.c
Modified	/trunk/madman/Rpacks/Rsubread/src/gene-algorithms.c
Modified	/trunk/madman/Rpacks/Rsubread/src/readSummary.c
Modified	/trunk/madman/Rpacks/Rsubread/src/subread.h
Modified	/trunk/madman/Rpacks/Rsubread/src/removeDupReads.h
Modified	/trunk/madman/Rpacks/Rsubread/src/SNPCalling.c
Modified	/trunk/madman/Rpacks/Rsubread/src/gene-algorithms.h
Modified	/trunk/madman/Rpacks/Rsubread/src/processExons.c
Modified	/trunk/madman/Rpacks/Rsubread/src/index-builder.c
Modified	/trunk/madman/Rpacks/Rsubread/src/gene-value-index.c

Revision 76846 by r.day

r.day — Thu, 23 May 2013 22:27:58 GMT

Bumped version, updated dates.

(Thu, 23 May 2013 22:27:58 GMT)

Modified

/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMappingAnalysis-dash-package.Rd

Revision 76845 by hpages

hpages — Thu, 23 May 2013 22:16:06 GMT

- Add explodeCigarOps() and explodeCigarOpLengths() low-level CIGAR utilities.
- 4x speed-up to cigarToRleList().
- Deprecate cigarToCigarTable() and summarizeCigarTable().

(Thu, 23 May 2013 22:16:06 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Modified	/trunk/madman/Rpacks/GenomicRanges/src/R_init_GenomicRanges.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/cigar_utils.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/GenomicRanges.h
Modified	/trunk/madman/Rpacks/GenomicRanges/man/cigar-utils.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R
Deleted	/trunk/madman/Rpacks/GenomicRanges/inst/scripts/cigar_summary.R

Revision 76843 by k.uziela

k.uziela — Thu, 23 May 2013 21:53:52 GMT

Added an option to return ExpressionSet and made it default output value

(Thu, 23 May 2013 21:53:52 GMT)

Modified	/trunk/madman/Rpacks/prebs/DESCRIPTION
Modified	/trunk/madman/Rpacks/prebs/vignettes/prebs.Rnw
Modified	/trunk/madman/Rpacks/prebs/R/PREBS.R
Modified	/trunk/madman/Rpacks/prebs/man/calc_prebs.Rd

Revision 76842 by v.obenchain

v.obenchain — Thu, 23 May 2013 21:05:01 GMT

Fix how 'missing' column is computed in 'colData' of SummarizedExperiment.
Cannot use filterBam() on a qname-sorted file.

(Thu, 23 May 2013 21:05:01 GMT)

Modified

/trunk/madman/Rpacks/Rsamtools/R/methods-BamFile.R

Revision 76841 by v.obenchain

v.obenchain — Thu, 23 May 2013 21:01:22 GMT

Update 'inter.feature' argument consequences in summarizeOverlaps() man page.

(Thu, 23 May 2013 21:01:22 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified	/trunk/madman/Rpacks/GenomicRanges/man/summarizeOverlaps.Rd

Revision 76840 by v.obenchain

v.obenchain — Thu, 23 May 2013 20:09:07 GMT

Clean up countBam() output in SummarizedExperiment 'colData'. Add number of
mapped reads.

(Thu, 23 May 2013 20:09:07 GMT)

Modified	/trunk/madman/Rpacks/Rsamtools/R/methods-BamFile.R
Modified	/trunk/madman/Rpacks/Rsamtools/DESCRIPTION

Revision 76839 by r.day

r.day — Thu, 23 May 2013 20:07:34 GMT

Modified all Rd files to pass CHECK without warnings.
Fixed NAMESPACE exports.
Roxygen2-style documentation for IdMap-- seems ok so far.

Bumped version, updated dates.

(Thu, 23 May 2013 20:07:34 GMT)

Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/to.base.Misc.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getBootstrap.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/aligned.IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/textBoundingBox.Display.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/plot.Bootstrap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/byRowNames.Subset.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/primaryKey.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/secondaryKey.Mixture.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/minCountGroupConstraint.DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/Mixture.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/swapKeys.IdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/as.IdMap.UniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/as.UniquePairs.IdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getUniquePairs.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getSampleNames.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getName.IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getDiff.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/Subset.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/Corr.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getMatchInfo.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/R/idMapBase.R
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getCorrData.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getMapNames.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getUniquePairs.Corr.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/plot.Mixture.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/swapKeys.UniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/summary.IdMapDiffCounts.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getUniquePairs.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/pack.experiments.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/minCountConstraint.DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/CsvList.merge.Misc.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getMatchInfo.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/mixture.plot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getIdMapList.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getStats.IdMapCounts.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/interleave.Misc.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/as.data.frame.IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/do.glm.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/words.Misc.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/primaryKey.Mixture.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/corr.plot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/mixture.boxplot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/Misc.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/interactive.mixture.plot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getCompoundGroups.IdMapDiffCounts.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/subsetCorr.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/corr.boxplot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/as.MultiSet.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/interactive.corr.plot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/subsetData.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/interactive.mixture.boxplot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/boxplotdataJitter.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/plot.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/Bootstrap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/fisherTransformJacobean.DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/examples.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/diffCounts.plot.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/interactive.corr.boxplot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/plot.Corr.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getCorrDataFrame.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/secondaryKey.IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/fisherTransformInverse.DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMapCounts.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getCompoundEvents.IdMapDiffCounts.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/interactive.plot.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/merge.IdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getExperimentSet.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/000-LB-.IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/zoom.pars.Display.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/dim.IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getMapNames.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/equals.UniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/to.index.expr.Misc.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/boxplot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getUnionIdMap.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getMatch.UniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/as.data.frame.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/interactive.plot.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/plot.IdMapCounts.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/do.apply.DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getCounts.IdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/DESCRIPTION
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/removeNASeries.DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getMixture.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/UniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/Display.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getData.Mixture.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/byRow.Subset.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/create.UniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/create.Display.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getCounts.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getData.Corr.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getCorr.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/minAvgCountConstraint.DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/copy.Display.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMapDiffCounts.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/progressMsg.Display.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/line.loess.Display.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/primaryKey.IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/IdMapDiff.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/clust.Mixture.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/R/display.R
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/fisherTransform.DataFilter.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/getStats.Mixture.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/byColumn.Subset.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/plot.IdMapDiffCounts.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/line.unsorted.Display.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/secondaryKey.CorrData.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/byColNames.Subset.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/R/dataFilter.R
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/as.list.IdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/primaryIDs.IdMapBase.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/to.binary.logical.Misc.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/unique.UniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/ecdf.plot.JointIdMap.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/R/idMap.R
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/subsetGroups.JointUniquePairs.Rd
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/NAMESPACE
Modified	/trunk/madman/Rpacks/IdMappingAnalysis/man/dimnames.IdMapBase.Rd

Revision 76838 by m.love

m.love — Thu, 23 May 2013 20:04:19 GMT

improved estimation of prior variance for low residual
degrees of freedom; option to use t-distribution for null

(Thu, 23 May 2013 20:04:19 GMT)

Modified	/trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified	/trunk/madman/Rpacks/DESeq2/R/core.R
Modified	/trunk/madman/Rpacks/DESeq2/man/nbinomWaldTest.Rd

Revision 76836 by v.obenchain

v.obenchain — Thu, 23 May 2013 18:49:03 GMT

Add check for 'use.names' and clarify check for 'yieldSize' in
readGAlignmentsListFromBam().

(Thu, 23 May 2013 18:49:03 GMT)

Modified

/trunk/madman/Rpacks/Rsamtools/R/methods-BamFile.R

Revision 76835 by v.obenchain

v.obenchain — Thu, 23 May 2013 18:47:30 GMT

Allow readGAlignmentPairs() to accept a BamFile as 'file'.

(Thu, 23 May 2013 18:47:30 GMT)

Modified

/trunk/madman/Rpacks/GenomicRanges/R/GAlignmentPairs-class.R

Revision 76834 by l.chavez

l.chavez — Thu, 23 May 2013 17:46:26 GMT

MEDIPS.selectROIs bug fix

(Thu, 23 May 2013 17:46:26 GMT)

Modified	/trunk/madman/Rpacks/MEDIPS/R/MEDIPS.selectROIs.R
Modified	/trunk/madman/Rpacks/MEDIPS/DESCRIPTION

Revision 76832 by v.obenchain

v.obenchain — Thu, 23 May 2013 15:59:06 GMT

Update BamFile man page description of how 'inter.feature' affects counting with
summarizeOverlaps(().

(Thu, 23 May 2013 15:59:06 GMT)

Modified

/trunk/madman/Rpacks/Rsamtools/man/BamFile-class.Rd

Revision 76830 by j.barry

j.barry — Thu, 23 May 2013 13:54:47 GMT

getTopTable output of multi-channel data

(Thu, 23 May 2013 13:54:47 GMT)

Modified	/trunk/madman/Rpacks/cellHTS2/DESCRIPTION
Modified	/trunk/madman/Rpacks/cellHTS2/CHANGES
Modified	/trunk/madman/Rpacks/cellHTS2/R/getTopTable.R

Revision 76829 by m.stadler

m.stadler — Thu, 23 May 2013 09:35:38 GMT

added section on file storage locations to vignette; bumped minor version

(Thu, 23 May 2013 09:35:38 GMT)

Modified	/trunk/madman/Rpacks/QuasR/DESCRIPTION
Modified	/trunk/madman/Rpacks/QuasR/vignettes/QuasR-Overview.Rnw

Revision 76828 by m.kohl

m.kohl — Thu, 23 May 2013 06:13:16 GMT

added matrix method for function selectHKs

(Thu, 23 May 2013 06:13:16 GMT)

Modified	/trunk/madman/Rpacks/NormqPCR/DESCRIPTION
Modified	/trunk/madman/Rpacks/NormqPCR/man/selectHKs.Rd
Modified	/trunk/madman/Rpacks/NormqPCR/R/selectHKs.R
Modified	/trunk/madman/Rpacks/NormqPCR/man/NormqPCR-package.Rd
Modified	/trunk/madman/Rpacks/NormqPCR/man/deltaDeltaCt.Rd

Revision 76826 by p.murrell

p.murrell — Thu, 23 May 2013 03:23:32 GMT

fix R verion check in drawEdge()

(Thu, 23 May 2013 03:23:32 GMT)

Modified	/trunk/madman/Rpacks/hyperdraw/inst/NEWS.Rd
Modified	/trunk/madman/Rpacks/hyperdraw/R/draw.R

Revision 76825 by y.liao

y.liao — Thu, 23 May 2013 02:07:11 GMT

A bug in featureCounts fixed: the -B option should set 1 not 0.

(Thu, 23 May 2013 02:07:11 GMT)

Modified

/trunk/madman/Rpacks/Rsubread/src/readSummary.c

Revision 76823 by h.bengtsson

h.bengtsson — Thu, 23 May 2013 01:19:22 GMT

DOCUMENTATION: Dropped an extra 'both' in the help page of normalizeAffine().

(Thu, 23 May 2013 01:19:22 GMT)

Modified	/trunk/madman/Rpacks/aroma.light/man/normalizeAffine.matrix.Rd
Modified	/trunk/madman/Rpacks/aroma.light/Makefile
Modified	/trunk/madman/Rpacks/aroma.light/R/normalizeAffine.matrix.R

Revision 76822 by khansen

khansen — Thu, 23 May 2013 01:08:16 GMT

fixes to plotRegions/plotManyRegions and plot.BSseqTstat

(Thu, 23 May 2013 01:08:16 GMT)

Modified	/trunk/madman/Rpacks/bsseq/R/plotting.R
Modified	/trunk/madman/Rpacks/bsseq/DESCRIPTION
Modified	/trunk/madman/Rpacks/bsseq/R/dmrFinder.R
Modified	/trunk/madman/Rpacks/bsseq/inst/NEWS.Rd
Modified	/trunk/madman/Rpacks/bsseq/R/BSseq_utils.R

Revision 76821 by sdurinck

sdurinck — Wed, 22 May 2013 23:26:29 GMT

Using native BioMart header info to name column names of getBM result

(Wed, 22 May 2013 23:26:29 GMT)

Modified	/trunk/madman/Rpacks/biomaRt/DESCRIPTION
Modified	/trunk/madman/Rpacks/biomaRt/R/biomaRt.R

Revision 76816 by m.mccall

m.mccall — Wed, 22 May 2013 00:00:00 GMT

fixed minor bug in tnetfuncs.cc

(Wed, 22 May 2013 00:00:00 GMT)

Modified	/trunk/madman/Rpacks/ternarynet/DESCRIPTION
Modified	/trunk/madman/Rpacks/ternarynet/src/tnetfuncs.cc

Revision 76813 by l.zhu

l.zhu — Wed, 22 May 2013 20:49:30 GMT

fixed makeVennDiagram nooverlap problem on May 22 2013

(Wed, 22 May 2013 20:49:30 GMT)

Modified	/trunk/madman/Rpacks/ChIPpeakAnno/DESCRIPTION
Modified	/trunk/madman/Rpacks/ChIPpeakAnno/R/makeVennDiagram.R
Modified	/trunk/madman/Rpacks/ChIPpeakAnno/R/findOverlappingPeaks.R

Revision 76812 by v.obenchain

v.obenchain — Wed, 22 May 2013 19:43:08 GMT

Modify 'colData' slot of SummarizedExperiment output from summarizeOverlaps().
This now holds the class type and length of 'reads'.

(Wed, 22 May 2013 19:43:08 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified	/trunk/madman/Rpacks/GenomicRanges/man/summarizeOverlaps.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/R/summarizeOverlaps.R

Revision 76811 by k.horan

k.horan — Wed, 22 May 2013 19:25:30 GMT

hopefully a fix for building on windows

(Wed, 22 May 2013 19:25:30 GMT)

Modified	/trunk/madman/Rpacks/eiR/src/f2c/Makefile
Modified	/trunk/madman/Rpacks/eiR/src/f2c/main.c
Modified	/trunk/madman/Rpacks/eiR/src/Makevars.win

Revision 76810 by k.horan

k.horan — Wed, 22 May 2013 19:25:23 GMT

new version for similarity update

(Wed, 22 May 2013 19:25:23 GMT)

Modified

/trunk/madman/Rpacks/eiR/DESCRIPTION

Revision 76809 by k.horan

k.horan — Wed, 22 May 2013 19:25:15 GMT

finished adding option to return similarity results

(Wed, 22 May 2013 19:25:15 GMT)

Modified	/trunk/madman/Rpacks/eiR/man/eiCluster.Rd
Modified	/trunk/madman/Rpacks/eiR/inst/unitTests/test_main.R
Modified	/trunk/madman/Rpacks/eiR/man/eiQuery.Rd
Modified	/trunk/madman/Rpacks/eiR/R/core.R

Revision 76808 by p.mcmurdie

p.mcmurdie — Wed, 22 May 2013 18:44:47 GMT

phyloseq 1.5.17 - rarefy_even_depth(), and minor improvements

(Wed, 22 May 2013 18:44:47 GMT)

Modified	/trunk/madman/Rpacks/phyloseq/inst/NEWS
Modified	/trunk/madman/Rpacks/phyloseq/R/transform_filter-methods.R
Modified	/trunk/madman/Rpacks/phyloseq/DESCRIPTION
Added	/trunk/madman/Rpacks/phyloseq/inst/tests/test-rarefy.R
Modified	/trunk/madman/Rpacks/phyloseq/man/rarefy_even_depth.Rd

Revision 76806 by l.chavez

l.chavez — Wed, 22 May 2013 17:50:46 GMT

Manual update: ratio direction

(Wed, 22 May 2013 17:50:46 GMT)

Modified	/trunk/madman/Rpacks/MEDIPS/R/MEDIPS.meth.R
Modified	/trunk/madman/Rpacks/MEDIPS/DESCRIPTION
Modified	/trunk/madman/Rpacks/MEDIPS/inst/doc/MEDIPS.Rnw

Revision 76805 by v.obenchain

v.obenchain — Wed, 22 May 2013 17:43:47 GMT

Add output of countBam() to 'colData' slot of SummarizedExperiment created by
summarizeOverlaps() with BamFile or BamFileList.

(Wed, 22 May 2013 17:43:47 GMT)

Modified	/trunk/madman/Rpacks/Rsamtools/R/methods-BamFile.R
Modified	/trunk/madman/Rpacks/Rsamtools/man/BamFile-class.Rd

Revision 76804 by p.shannon

p.shannon — Wed, 22 May 2013 16:49:18 GMT

fixed setNodeShapeDirect man page

(Wed, 22 May 2013 16:49:18 GMT)

Modified

/trunk/madman/Rpacks/RCytoscape/DESCRIPTION

Revision 76803 by p.shannon

p.shannon — Wed, 22 May 2013 16:47:33 GMT

added getNodeShapes to example

(Wed, 22 May 2013 16:47:33 GMT)

Modified

/trunk/madman/Rpacks/RCytoscape/man/setNodeShapeDirect.Rd

Revision 76802 by stvjc

stvjc — Wed, 22 May 2013 16:45:44 GMT

All.cis needs to match seqlevels of output ranges to names of smlSet smList

(Wed, 22 May 2013 16:45:44 GMT)

Modified	/trunk/madman/Rpacks/GGtools/R/fdr.all.cis.R
Modified	/trunk/madman/Rpacks/GGtools/DESCRIPTION

Revision 76801 by p.shannon

p.shannon — Wed, 22 May 2013 16:38:57 GMT

fixed see also type

(Wed, 22 May 2013 16:38:57 GMT)

Modified

/trunk/madman/Rpacks/RCytoscape/man/setNodeShapeDirect.Rd

Revision 76800 by v.haberle

v.haberle — Wed, 22 May 2013 16:30:15 GMT

Added NEWS file

(Wed, 22 May 2013 16:30:15 GMT)

Added

/trunk/madman/Rpacks/CAGEr/NEWS

Revision 76799 by v.haberle

v.haberle — Wed, 22 May 2013 16:26:22 GMT

Fixed column classes in CTSS data.frame when reading the data from bam files

(Wed, 22 May 2013 16:26:22 GMT)

Modified	/trunk/madman/Rpacks/CAGEr/R/ImportMethods.R
Modified	/trunk/madman/Rpacks/CAGEr/DESCRIPTION
Modified	/trunk/madman/Rpacks/CAGEr/man/getCTSS.Rd

Revision 76797 by t.yates

t.yates — Wed, 22 May 2013 14:54:24 GMT

Updated cookbook to include cds example. v1.3.2

(Wed, 22 May 2013 14:54:24 GMT)

Modified	/trunk/madman/Rpacks/annmap/DESCRIPTION
Modified	/trunk/madman/Rpacks/annmap/inst/cookbook/cookbook.Rnw

Revision 76796 by t.yates

t.yates — Wed, 22 May 2013 14:54:12 GMT

Allow transcriptCoordsToGenome to take CDS region into account

(Wed, 22 May 2013 14:54:12 GMT)

Modified	/trunk/madman/Rpacks/annmap/R/coords.R
Modified	/trunk/madman/Rpacks/annmap/man/annmap.coords.Rd

Revision 76795 by whuber

whuber — Wed, 22 May 2013 12:16:25 GMT

Fixed a typo and some minor reformatting of comments.

(Wed, 22 May 2013 12:16:25 GMT)

Modified	/trunk/madman/Rpacks/cellHTS2/R/readPlateList.R
Modified	/trunk/madman/Rpacks/cellHTS2/R/methods-cellHTS.R
Modified	/trunk/madman/Rpacks/cellHTS2/DESCRIPTION

Revision 76794 by m.mccall

m.mccall — Wed, 22 May 2013 04:19:23 GMT

altered default values in tnetpost

(Wed, 22 May 2013 04:19:23 GMT)

Modified	/trunk/madman/Rpacks/ternarynet/R/attractorSummary.R
Modified	/trunk/madman/Rpacks/ternarynet/R/plotFit.R
Modified	/trunk/madman/Rpacks/ternarynet/DESCRIPTION
Modified	/trunk/madman/Rpacks/ternarynet/man/tnetpost.Rd
Modified	/trunk/madman/Rpacks/ternarynet/R/tnetpost.R

Revision 76792 by y.liao

y.liao — Tue, 21 May 2013 23:24:44 GMT

Trimming spaces before gene_id

(Tue, 21 May 2013 23:24:44 GMT)

Modified

/trunk/madman/Rpacks/Rsubread/src/readSummary.c

Revision 76790 by r.tautenhahn

r.tautenhahn — Tue, 21 May 2013 23:16:16 GMT

fixed bug in patternVsRowScore (group.nearest) that was introduced by the
modifications in rev 65169 and caused features to be aligned that were far outside the given m/z and retention time windows.

(Tue, 21 May 2013 23:16:16 GMT)

Modified

/trunk/madman/Rpacks/xcms/inst/NEWS

Revision 76789 by r.tautenhahn

r.tautenhahn — Tue, 21 May 2013 23:12:18 GMT

fixed bug in patternVsRowScore (group.nearest) that was introduced by the
modifications in rev 65169 and caused features to be aligned that were far outside the given m/z and retention time windows.

(Tue, 21 May 2013 23:12:18 GMT)

Modified

/trunk/madman/Rpacks/xcms/DESCRIPTION

Revision 76788 by r.tautenhahn

r.tautenhahn — Tue, 21 May 2013 23:10:35 GMT

fixed bug in patternVsRowScore (group.nearest) that was introduced by the
modifications in rev 65169 and caused features to be aligned that were far outside the given m/z and retention time windows.

(Tue, 21 May 2013 23:10:35 GMT)

Modified

/trunk/madman/Rpacks/xcms/R/xcmsSet.R

Revision 76787 by v.obenchain

v.obenchain — Tue, 21 May 2013 00:00:00 GMT

readVcf() now creates rownames with format CHROM:POS_REF/ALT for variants with ID=".".

(Tue, 21 May 2013 00:00:00 GMT)

Modified	/trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified	/trunk/madman/Rpacks/VariantAnnotation/src/vcffile.c
Modified	/trunk/madman/Rpacks/VariantAnnotation/man/readVcf-methods.Rd

Revision 76785 by t.yin

t.yin — Tue, 21 May 2013 00:00:00 GMT

add cbind/rbind for tracks object and change top margin to 1

(Tue, 21 May 2013 00:00:00 GMT)

Modified	/trunk/madman/Rpacks/ggbio/man/tracks.Rd
Modified	/trunk/madman/Rpacks/ggbio/R/tracks.R

Revision 76784 by t.yin

t.yin — Tue, 21 May 2013 19:48:04 GMT

Add combination methods for tracks and add get_gtable function to get gtable from tracks object. 

(Tue, 21 May 2013 19:48:04 GMT)

Modified	/trunk/madman/Rpacks/ggbio/man/tracks.Rd
Modified	/trunk/madman/Rpacks/ggbio/R/tracks.R
Modified	/trunk/madman/Rpacks/ggbio/NAMESPACE
Modified	/trunk/madman/Rpacks/ggbio/R/Plot-class.R

Revision 76780 by v.haberle

v.haberle — Tue, 21 May 2013 15:59:29 GMT

Allowed use of custom built genomes by excluding the check of presence of genome name in the available.genomes list

(Tue, 21 May 2013 15:59:29 GMT)

Modified	/trunk/madman/Rpacks/CAGEr/DESCRIPTION
Modified	/trunk/madman/Rpacks/CAGEr/R/AllClasses.R
Modified	/trunk/madman/Rpacks/CAGEr/inst/doc/CAGEr.Rnw

Revision 76779 by n.servant

n.servant — Tue, 21 May 2013 15:20:15 GMT

small bugs fixed

(Tue, 21 May 2013 15:20:15 GMT)

Modified	/trunk/madman/Rpacks/HiTC/R/import.R
Modified	/trunk/madman/Rpacks/HiTC/NEWS
Modified	/trunk/madman/Rpacks/HiTC/man/importC.Rd
Modified	/trunk/madman/Rpacks/HiTC/R/HTCexp-class.R
Modified	/trunk/madman/Rpacks/HiTC/man/mapC.Rd
Modified	/trunk/madman/Rpacks/HiTC/R/mapC.R
Modified	/trunk/madman/Rpacks/HiTC/DESCRIPTION

Revision 76778 by khansen

khansen — Tue, 21 May 2013 14:59:45 GMT

added RatioSet class and ratioConvert() method

(Tue, 21 May 2013 14:59:45 GMT)

Modified	/trunk/madman/Rpacks/minfi/man/mapToGenome-methods.Rd
Modified	/trunk/madman/Rpacks/minfi/NAMESPACE
Added	/trunk/madman/Rpacks/minfi/man/RatioSet-class.Rd
Modified	/trunk/madman/Rpacks/minfi/inst/NEWS.Rd
Added	/trunk/madman/Rpacks/minfi/R/rset.R
Added	/trunk/madman/Rpacks/minfi/man/ratioConvert-methods.Rd
Modified	/trunk/madman/Rpacks/minfi/R/generics.R
Modified	/trunk/madman/Rpacks/minfi/R/gmset.R
Modified	/trunk/madman/Rpacks/minfi/man/MethylSet-class.Rd
Modified	/trunk/madman/Rpacks/minfi/man/GenomicMethylSet-class.Rd
Modified	/trunk/madman/Rpacks/minfi/DESCRIPTION
Modified	/trunk/madman/Rpacks/minfi/R/grset.R
Modified	/trunk/madman/Rpacks/minfi/R/mset.R

Revision 76777 by a.honkela

a.honkela — Tue, 21 May 2013 12:13:19 GMT

tigre 1.15.1: bug fixes to non-cascade model (identical to tigre 1.14.1)

(Tue, 21 May 2013 12:13:19 GMT)

Modified	/trunk/madman/Rpacks/tigre/DESCRIPTION
Modified	/trunk/madman/Rpacks/tigre/R/GPrank.R
Modified	/trunk/madman/Rpacks/tigre/R/gpsimLinearFunctions.R
Modified	/trunk/madman/Rpacks/tigre/R/GPPlot.R
Modified	/trunk/madman/Rpacks/tigre/inst/NEWS

Revision 76775 by r.stojnic

r.stojnic — Tue, 21 May 2013 10:58:04 GMT

Fixed a typo

(Tue, 21 May 2013 10:58:04 GMT)

Modified

/trunk/madman/Rpacks/PWMEnrich/R/MotifEnrichmentResults-methods.R

Revision 76772 by radivot

radivot — Tue, 21 May 2013 09:50:44 GMT

fixed sod example. Source of integration instability was my clipping of negative concentrations to zero. So I fixed simulate to no longer do this. 

(Tue, 21 May 2013 09:50:44 GMT)

Modified	/trunk/madman/Rpacks/SBMLR/R/simulate.r
Added	/trunk/madman/Rpacks/SBMLR/inst/models/sbmlrDemo.R
Modified	/trunk/madman/Rpacks/SBMLR/inst/models/sod.xml
Modified	/trunk/madman/Rpacks/SBMLR/inst/models/sod.R
Modified	/trunk/madman/Rpacks/SBMLR/inst/models/sodNatural.R

Revision 76771 by t.yin

t.yin — Tue, 21 May 2013 05:47:50 GMT

fix tracks bugs for labeling and remove Grob class subclass, this may be confusing

(Tue, 21 May 2013 05:47:50 GMT)

Modified	/trunk/madman/Rpacks/ggbio/R/tracks.R
Modified	/trunk/madman/Rpacks/ggbio/R/Grob-class.R
Modified	/trunk/madman/Rpacks/ggbio/R/Tracked-class.R
Modified	/trunk/madman/Rpacks/ggbio/R/Plot-class.R

Revision 76770 by t.yin

t.yin — Tue, 21 May 2013 03:56:42 GMT

add fix arguments

(Tue, 21 May 2013 03:56:42 GMT)

Modified	/trunk/madman/Rpacks/biovizBase/R/addStepping-method.R
Modified	/trunk/madman/Rpacks/biovizBase/man/addStepping-method.Rd

Revision 76768 by h.bengtsson

h.bengtsson — Tue, 21 May 2013 02:08:09 GMT

Version: 1.33.1 [2013-05-20]
o Same updates as in release v1.32.1.

Version: 1.32.1 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long. 

(Tue, 21 May 2013 02:08:09 GMT)

Modified	/trunk/madman/Rpacks/affxparser/man/convertCdf.Rd
Modified	/trunk/madman/Rpacks/affxparser/man/readCdfDataFrame.Rd
Modified	/trunk/madman/Rpacks/affxparser/Makefile
Modified	/trunk/madman/Rpacks/affxparser/man/readCcgHeader.Rd
Modified	/trunk/madman/Rpacks/affxparser/man/readCelUnits.Rd
Modified	/trunk/madman/Rpacks/affxparser/DESCRIPTION
Modified	/trunk/madman/Rpacks/affxparser/man/convertCel.Rd
Modified	/trunk/madman/Rpacks/affxparser/man/updateCel.Rd
Modified	/trunk/madman/Rpacks/affxparser/man/arrangeCelFilesByChipType.Rd
Modified	/trunk/madman/Rpacks/affxparser/man/readCdfCellIndices.Rd
Modified	/trunk/madman/Rpacks/affxparser/inst/NEWS
Modified	/trunk/madman/Rpacks/affxparser/man/readCdfUnits.Rd