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Revision: 101284
Author: c.fletez-brant
Date: 2015-03-27T12:56:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowClean/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowClean/R/flowClean.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1e602837d25e2ca5502ea5e6eb57b385a0245ea8

    fixed warning

Revision: 101283
Author: g.ball
Date: 2015-03-27T12:47:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/STATegRa/DESCRIPTION
Modified  /trunk/madman/Rpacks/STATegRa/NAMESPACE
Modified  /trunk/madman/Rpacks/STATegRa/R/STATegRa_fused.R
Modified  /trunk/madman/Rpacks/STATegRa/R/STATegRa_omicsCLUST_bioDist.R
Modified  /trunk/madman/Rpacks/STATegRa/R/STATegRa_omicsCLUST_bioDistW.R
Modified  /trunk/madman/Rpacks/STATegRa/R/STATegRa_omicsCLUST_bioMap.R
Modified  /trunk/madman/Rpacks/STATegRa/R/STATegRa_omicsPCA_caClass.R
Modified  /trunk/madman/Rpacks/STATegRa/R/STATegRa_omicsPCA_methods.R
Modified  /trunk/madman/Rpacks/STATegRa/R/STATegRa_omicsPCA_plotting.R
Added  /trunk/madman/Rpacks/STATegRa/R/STATegRa_package.R
Added  /trunk/madman/Rpacks/STATegRa/man/PCA.selection.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/STATegRa.Rd
Modified  /trunk/madman/Rpacks/STATegRa/man/STATegRaUsersGuide.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_InitialData.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_PCA.selection.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_VAF.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioDist.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioDistFeature.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioDistFeaturePlot.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioDistW-plot.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioDistW.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioDistclass-constructor.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioDistclass.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioMap-class.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_bioMap-constructor.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_biplotRes.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_caClass.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_createOmicsExpressionSet.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/STATegRa_data.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_initial_data.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_loadings.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_methodInfo.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_modelSelection.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_omicsCompAnalysis.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_package.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_plotRes.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_plotVAF.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_preprocessing.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_scores.Rd
Deleted  /trunk/madman/Rpacks/STATegRa/man/STATegRa_selectCommonComps.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/bioDist.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/bioDistFeature.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/bioDistFeaturePlot.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/bioDistW.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/bioDistWPlot.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/bioDistclass.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/bioMap.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/biplotRes.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/caClass-class.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/createOmicsExpressionSet.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/getInitialData.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/getLoadings.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/getMethodInfo.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/getPreprocessing.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/getScores.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/getVAF.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/modelSelection.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/omicsCompAnalysis.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/plotRes.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/plotVAF.Rd
Added  /trunk/madman/Rpacks/STATegRa/man/selectCommonComps.Rd
Version 1.1.0-git8f5d490
Revision: 101282
Author: m.iterson
Date: 2015-03-27T11:47:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/MethylAid/DESCRIPTION
Modified  /trunk/madman/Rpacks/MethylAid/R/server.R
Modified  /trunk/madman/Rpacks/MethylAid/R/ui.R
Modified  /trunk/madman/Rpacks/MethylAid/R/uitext.R
Modified  /trunk/madman/Rpacks/MethylAid/R/util.R
modified shiny UI
Revision: 101281
Author: h.klein
Date: 2015-03-27T11:44:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/R453Plus1Toolbox/DESCRIPTION
Modified  /trunk/madman/Rpacks/R453Plus1Toolbox/NAMESPACE
fixed namespace issues 2
Revision: 101280
Author: j.larson
Date: 2015-03-27T11:24:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/ReportingTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/ReportingTools/NEWS
updated JL email
Revision: 101279
Author: j.larson
Date: 2015-03-27T11:20:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/npGSEA/DESCRIPTION
Modified  /trunk/madman/Rpacks/npGSEA/NEWS
Updated email and version to 1.3.8
Revision: 101278
Author: h.klein
Date: 2015-03-27T11:03:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/R453Plus1Toolbox/DESCRIPTION
Modified  /trunk/madman/Rpacks/R453Plus1Toolbox/NAMESPACE
fixed namespace issues
Revision: 101277
Author: n.kurbatova
Date: 2015-03-27T09:05:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/ontoCAT/DESCRIPTION
DESCRIPTION file changed
Revision: 101276
Author: n.kurbatova
Date: 2015-03-27T09:04:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/ontoCAT/DESCRIPTION
DESCRIPTION file changed
Revision: 101275
Author: h.froehlich
Date: 2015-03-27T08:14:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/birte/DESCRIPTION
Modified  /trunk/madman/Rpacks/birte/R/birteRun.R
Modified  /trunk/madman/Rpacks/birte/man/birteRun.Rd
Modified  /trunk/madman/Rpacks/birte/man/limmaAnalysis.Rd
Modified  /trunk/madman/Rpacks/birte/vignettes/birte.Rnw
added support for arbitrary design matrices
Revision: 101274
Author: t.peters
Date: 2015-03-27T08:08:24+00:00
Paths:
Added  /trunk/madman/Rpacks/DMRcate/CITATION
Modified  /trunk/madman/Rpacks/DMRcate/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0763a155246250d0ddeb29e9cf65a24540776513

    Merge remote-tracking branch 'origin/master'

    Conflicts:
    	DESCRIPTION


Commit id: 3369af65bc3ad7a2498650992c0ec211c535813e

    DMRcate_1.3.1

Revision: 101273
Author: hpages
Date: 2015-03-27T05:48:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/TxDb-class.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGFF.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_makeTxDbFromGRanges.R
Tweak makeTxDbFromGRanges() to no fail on the empty case (i.e. now it returns
a TxDb object with 0 transcripts if no transcripts can be extracted from the
input).
Revision: 101272
Author: j.storey
Date: 2015-03-27T05:05:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/qvalue/DESCRIPTION
Added date to DESCRIPTION.
Revision: 101271
Author: j.storey
Date: 2015-03-27T04:50:22+00:00
Paths:
Added  /trunk/madman/Rpacks/qvalue/inst/doc/qvalue.R
Added  /trunk/madman/Rpacks/qvalue/inst/doc/qvalue.Rnw
Added  /trunk/madman/Rpacks/qvalue/inst/doc/qvalue.pdf
Added several documents to inst/doc/
Revision: 101270
Author: j.storey
Date: 2015-03-27T04:49:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/qvalue/DESCRIPTION
Modified  /trunk/madman/Rpacks/qvalue/NAMESPACE
Added  /trunk/madman/Rpacks/qvalue/R/empPvals.R
Added  /trunk/madman/Rpacks/qvalue/R/hedenfalk.R
Added  /trunk/madman/Rpacks/qvalue/R/hist_qvalue.R
Added  /trunk/madman/Rpacks/qvalue/R/lfdr.R
Added  /trunk/madman/Rpacks/qvalue/R/multiplot.R
Added  /trunk/madman/Rpacks/qvalue/R/pi0est.R
Added  /trunk/madman/Rpacks/qvalue/R/plot_qvalue.R
Modified  /trunk/madman/Rpacks/qvalue/R/qvalue.R
Added  /trunk/madman/Rpacks/qvalue/R/summary_qvalue.R
Added  /trunk/madman/Rpacks/qvalue/R/write_qvalue.R
Added  /trunk/madman/Rpacks/qvalue/data/datalist
Modified  /trunk/madman/Rpacks/qvalue/data/hedenfalk.RData
Added  /trunk/madman/Rpacks/qvalue/inst/NEWS
Added  /trunk/madman/Rpacks/qvalue/inst/doc
Added  /trunk/madman/Rpacks/qvalue/man/empPvals.Rd
Added  /trunk/madman/Rpacks/qvalue/man/hedenfalk.Rd
Deleted  /trunk/madman/Rpacks/qvalue/man/hedenfalk.rd
Added  /trunk/madman/Rpacks/qvalue/man/hist.qvalue.Rd
Added  /trunk/madman/Rpacks/qvalue/man/lfdr.Rd
Added  /trunk/madman/Rpacks/qvalue/man/pi0est.Rd
Added  /trunk/madman/Rpacks/qvalue/man/plot.qvalue.Rd
Deleted  /trunk/madman/Rpacks/qvalue/man/qplot.rd
Deleted  /trunk/madman/Rpacks/qvalue/man/qsummary.rd
Added  /trunk/madman/Rpacks/qvalue/man/qvalue.Rd
Deleted  /trunk/madman/Rpacks/qvalue/man/qvalue.rd
Deleted  /trunk/madman/Rpacks/qvalue/man/qwrite.rd
Added  /trunk/madman/Rpacks/qvalue/man/summary.qvalue.Rd
Added  /trunk/madman/Rpacks/qvalue/man/write.qvalue.Rd
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/my-qvalue-results.txt
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/pHist.eps
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/pHist.pdf
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qHist.eps
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qHist.pdf
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qPlots.eps
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qPlots.pdf
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qvalue-002.eps
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qvalue-002.pdf
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qvalue-004.eps
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qvalue-004.pdf
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qvalue-006.eps
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qvalue-006.pdf
Modified  /trunk/madman/Rpacks/qvalue/vignettes/qvalue.Rnw
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/qvalue.bib
Added  /trunk/madman/Rpacks/qvalue/vignettes/qvaluerefs.bib
Major update to devel version 1.99 to be released as version 2.0. 
Revision: 101268
Author: l.zhu
Date: 2015-03-27T03:25:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/annotateOfftargets.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/filterOffTarget.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/findgRNAs.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/offTargetAnalysis.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/searchHits.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/uniqueREs.R
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/NEWS
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/gRNAProvidedSearchNOoffTarget/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/gRNAProvidedSearchNOoffTarget/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withRE/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withRE/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withRE/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withRE/pairedgRNAs.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withoutRE/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withoutRE/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withoutRE/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withoutRE/pairedgRNAs.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/recreateTestResults.R
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/RIPK1stopallgRNAs.fa
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/mRIPK1stop.gbk
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/pairedgRNAs.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/RIPK1stopallgRNAs.fa
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/mRIPK1stop.gbk
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/pairedgRNAs.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/RIPK1stopallgRNAs.fa
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/mRIPK1stop.gbk
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/pairedgRNAs.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withRE/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withRE/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withRE/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withRE/pairedgRNAs.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withoutRE/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withoutRE/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withoutRE/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withoutRE/pairedgRNAs.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/unitTests/test_mouse_orgAnn_annotateExon.R
Modified  /trunk/madman/Rpacks/CRISPRseek/man/offTargetAnalysis.Rd
Modified  /trunk/madman/Rpacks/CRISPRseek/man/searchHits.Rd
added parameter chromToExclude
Revision: 101267
Author: m.lawrence
Date: 2015-03-27T02:05:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/biovizBase/DESCRIPTION
version bump
Revision: 101266
Author: m.lawrence
Date: 2015-03-27T02:05:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/biovizBase/R/utils.R
carry over all mcols when computing the gaps; probably should not be
handling facets in this way at all, but anyway
Revision: 101262
Author: w.shi
Date: 2015-03-27T00:43:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/CHANGELOG
Modified  /trunk/madman/Rpacks/Rsubread/man/propmapped.Rd
updated documentation for propmapped function
Revision: 101260
Author: s.arora
Date: 2015-03-26T23:52:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
Added  /trunk/madman/Rpacks/AnnotationHubData/R/makeGSE62944ToExpressionSet.R
code update

- add tar.gz to allowed sourceTypes
- add recipe for GSE62944 To ExpressionSet
- add file to collate field of DESCRIPTION file
Revision: 101259
Author: s.arora
Date: 2015-03-26T23:50:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHubResource-class.R
code update

- add client code to handle ExpressionSets
Revision: 101257
Author: hpages
Date: 2015-03-26T23:43:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/DESCRIPTION
Modified  /trunk/madman/Rpacks/rtracklayer/R/gff.R
No more error when importing a GFF3 file results in an empty GRanges object
(either because the user specified non-existing types thru the 'feature.type'
argument of import(), or because the file contains no data).
Revision: 101256
Author: a.azad
Date: 2015-03-26T23:31:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowMatch/DESCRIPTION
Removes the constrain : Sample size is not equal to the summation of all cluster size
Revision: 101255
Author: a.azad
Date: 2015-03-26T23:29:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowMatch/R/ClusteredSample-class.R
Modified  /trunk/madman/Rpacks/flowMatch/src/MinWghtEdgCoverBipartite.cpp
Removes the constrain : Sample size is not equal to the summation of all cluster size
Revision: 101254
Author: m.lawrence
Date: 2015-03-26T23:26:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/NAMESPACE
screw it, just import all of GenomeInfoDb
Revision: 101253
Author: m.lawrence
Date: 2015-03-26T23:22:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/NAMESPACE
import Seqinfo from GenomeInfoDb
Revision: 101252
Author: j.gadin
Date: 2015-03-26T23:14:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ASEset-class.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/GlobalAnalysis-class.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions-visuals.R
Deleted  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/deprecations.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/mapbias-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-class.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEsetFromBam.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/GlobalAnalysis-class.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/barplot-lattice-support.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/countAllelesFromBam.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/coverageMatrixListFromGAL.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/gba.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAreaFromGeneNames.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getSnpIdFromLocation.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/man/implodeList-old.Rd
Deleted  /trunk/madman/Rpacks/AllelicImbalance/man/implodeList.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/makeMaskedFasta.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/vignettes/AllelicImbalance-vignette.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b2c234402e4052d2347c27a4e4f31a7bf369d4ac

    cleared the R CMD check errors


Commit id: a52d701e5c5b8404c60da5089c85a59fddcd2a3e

    cleared the R CMD build errors


Commit id: 51d32a07937b623bb1ec23da4c9fcee80d4ab2a6

    Merge branch 'changesToMethods'


Commit id: be4b002a1f05c3dd7f755d94ff973144f439ca7d

    removed auxillary functions


Commit id: 237850c012bd3d71888630e3359e85dbd360ad99

    all functions on auxillary-functions transferred to S4


Commit id: 0d02574b0a543e345dc2fe0dca372566a447450a

    countAllelesFromBam to S4


Commit id: 2d8aba8a9e260b85977a49ee2b736444bfe270ed

    getAreaFromGeneNames to S4


Commit id: 3c519390b279e19bf175ace8d4e8da67676f0a0a

    getAreaFromGeneNames to S4


Commit id: 7f578c4775483ba7232034f0a53c3f62fb42d79a

    merge with master


Commit id: d10f50aa2995af653fa59fb182df007c60d2685a

    ref and alt accessor

Revision: 101251
Author: m.lawrence
Date: 2015-03-26T23:13:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/geom_alignment-method.R
Fix the invalid message about the type column not matching any valid values
Revision: 101250
Author: m.lawrence
Date: 2015-03-26T23:12:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/geom_arrow-method.R
ensure that the arrow width is always at least 1; at least it avoids
an error
Revision: 101249
Author: n.hayden
Date: 2015-03-26T23:09:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/PAPi/DESCRIPTION
Modified  /trunk/madman/Rpacks/PAPi/R/papi.R
Modified  /trunk/madman/Rpacks/PAPi/man/papiHtest.Rd
Modified  /trunk/madman/Rpacks/PAPi/man/papiLine.Rd
forward-port changes from release
Revision: 101248
Author: m.carlson
Date: 2015-03-26T22:59:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/OrganismDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/OrganismDbi/man/OrganismDb.Rd
Modified  /trunk/madman/Rpacks/OrganismDbi/man/coordinate-mapping-method.Rd
Fixes bad link problems in man page.
Revision: 101247
Author: y.chen
Date: 2015-03-26T22:59:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/R/glmTreat.R
Modified  /trunk/madman/Rpacks/edgeR/R/topTags.R
Modified  /trunk/madman/Rpacks/edgeR/inst/NEWS.Rd
edgeR 3.9.14
- Update NEWS.Rd
- glmTreat() now returns same results as glmQLFTest() when lfc=0
Revision: 101246
Author: x.zheng
Date: 2015-03-26T22:56:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/HIBAG/DESCRIPTION
Modified  /trunk/madman/Rpacks/HIBAG/src/LibHLA.h
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a0ac2cec921a861afbf14d02fdb71ff3200e25dd

    C macro "__POPCNT__"

Revision: 101245
Author: d.tenenbaum
Date: 2015-03-26T22:55:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/chromDraw/DESCRIPTION
fix malformed DESCRIPTION
Revision: 101244
Author: hpages
Date: 2015-03-26T22:50:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/NAMESPACE
add missing import (dbconn from AnnotationDbi)
Revision: 101243
Author: m.lawrence
Date: 2015-03-26T22:49:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantTools/R/variantConcordance.R
SingleVariantFilter now does the right thing
Revision: 101241
Author: hpages
Date: 2015-03-26T21:56:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_makeTxDbFromGFF.R
use 'organism' arg instead of 'species' in makeTxDbFromGFF() unit tests
Revision: 101240
Author: hpages
Date: 2015-03-26T21:53:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/TxDb-class.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGFF.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/TxDb-class.Rd
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/makeTxDb.Rd
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/makeTxDbFromGFF.Rd
- Deprecate species() accessor in favor of organism() on TxDb objects.
- makeTxDbFromGFF(): deprecate 'species' arg in favor of new 'organism' arg.
Revision: 101239
Author: n.hayden
Date: 2015-03-26T21:36:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/npGSEA/DESCRIPTION
Modified  /trunk/madman/Rpacks/npGSEA/R/miscFunctions.R
remove non-ASCII character (looked like just a space)
Revision: 101238
Author: mtmorgan
Date: 2015-03-26T21:30:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
revert minor DESCRIPTION change
Revision: 101237
Author: mtmorgan
Date: 2015-03-26T21:14:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/src/bam_data.c
parse '=' correctly
Revision: 101236
Author: x.zheng
Date: 2015-03-26T21:12:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/inst/include/CoreDEF.h
Modified  /trunk/madman/Rpacks/gdsfmt/src/CoreArray/dPlatform.cpp
Modified  /trunk/madman/Rpacks/gdsfmt/src/gdsfmt.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 26dd78c493e317ddb96591537a9a82e0052bb22e

    C macro FMA4

    * C macro COREARRAY_CALL_ALIGN16_ARG ==> COREARRAY_CALL_ALIGN

Revision: 101235
Author: hpages
Date: 2015-03-26T20:33:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/BSgenomeForge.R
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Amellifera.BeeBase.assembly4-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Amellifera.UCSC.apiMel2-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.04232008-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR9-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau3-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau4-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau6-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau8-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Celegans.UCSC.ce10-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Celegans.UCSC.ce2-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Celegans.UCSC.ce6-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Cfamiliaris.UCSC.canFam2-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Cfamiliaris.UCSC.canFam3-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Dmelanogaster.UCSC.dm2-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Dmelanogaster.UCSC.dm3-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Dmelanogaster.UCSC.dm6-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer5-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer6-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer7-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Ecoli.NCBI.20080805-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Gaculeatus.UCSC.gasAcu1-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal3-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal4-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.GRCh38-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg17-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg18-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg19-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg38-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Mfuro.UCSC.musFur1-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac2-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac3-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm10-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm8-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm9-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro2-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro3-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn4-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn5-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn6-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Scerevisiae.UCSC.sacCer1-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Scerevisiae.UCSC.sacCer2-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Scerevisiae.UCSC.sacCer3-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Sscrofa.UCSC.susScr3-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Tguttata.UCSC.taeGut1-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.influenza.NCBI.20100628-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/bump_seed_version.sh
Modified  /trunk/madman/Rpacks/BSgenome/inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/inst/pkgtemplates/BSgenome_datapkg/R/zzz.R
Modified  /trunk/madman/Rpacks/BSgenome/inst/pkgtemplates/BSgenome_datapkg/man/package.Rd
Modified  /trunk/madman/Rpacks/BSgenome/inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/inst/pkgtemplates/MaskedBSgenome_datapkg/man/package.Rd
Modified  /trunk/madman/Rpacks/BSgenome/vignettes/BSgenomeForge.Rnw
Replace 'species' field with 'common_name' in BSgenome data package seed and
DESCRIPTION files.
Revision: 101233
Author: hpages
Date: 2015-03-26T20:26:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/GenomeDescription-class.R
minor tweak to deprecation message
Revision: 101232
Author: mtmorgan
Date: 2015-03-26T20:20:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
minor DESCRIPTION change
Revision: 101231
Author: j.hester
Date: 2015-03-26T20:03:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/R453Plus1Toolbox/R/ava2vcf.R
Update VCF rowData argument to rowRanges

This brings R453Plus1Toolbox in sync with r101004
Revision: 101230
Author: x.zheng
Date: 2015-03-26T19:32:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/R/Methods-SeqVarGDSClass.R
Modified  /trunk/madman/Rpacks/SeqArray/inst/unitTests/test_asVCF.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2c06383dbc493fda43d91514458b357c2fd66078

    Merge pull request #5 from smgogarten/master

    replace rowData with rowRanges

Commit id: 5433483401eb8a5021a892c3b183105fb0f3e700

    replace rowData with rowRanges

Revision: 101229
Author: hpages
Date: 2015-03-26T19:16:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/NAMESPACE
Modified  /trunk/madman/Rpacks/BSgenome/R/BSgenome-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/SNPlocs-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/XtraSNPlocs-class.R
Modified  /trunk/madman/Rpacks/BSgenome/man/SNPlocs-class.Rd
Modified  /trunk/madman/Rpacks/BSgenome/man/XtraSNPlocs-class.Rd
Some changes in response to latest changes in GenomeInfoDb (commit 101228):
- Replace species() accessor for SNPlocs and XtraSNPlocs objects with
  commonName(). Keep and deprecate the former in favor of the latter.
- Tweak the BSgenome() constructor in order to preserve backward compatibility
  with existing BSgenome packages.
Revision: 101228
Author: hpages
Date: 2015-03-26T19:09:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/GenomeDescription-class.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/GenomeDescription-class.Rd
Replace species() accessor for GenomeDescription objects with commonName().
Keep and deprecate the former in favor of the latter.
Revision: 101227
Author: m.jiang
Date: 2015-03-26T19:07:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingHierarchy-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingSet-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/inst/cppTest/unitTest/testSuite.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/inst/tests/InternalTestSuite.R
Modified  /trunk/madman/Rpacks/flowWorkspace/src/R_GatingHierarchy.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/gate.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/include/gate.hpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/include/transformation.hpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/macFlowJoWorkspace.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/transformation.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 89eb24b7f269781fe62fa5ad71ed3fae7d35c942

    Merge branch 'trunk'


Commit id: 1618164a2278ec69c4040280e45df2b522baf663

    implement inverse transformation for fasinh. close #142


Commit id: 4d57bbab17bba9a949f9c9a6629a04f3f426dc55

    use inverse transformation in speical scale of 256 to restore raw gate scale for EllipsoidGate.  #142


Commit id: 9f7bd71037bee5022e54c56bf4fab4dc868750b6

    implement getInverseTransformation API at c++ level


Commit id: 9464ca1d2a556a1e7a3d1351465cc20ada422be9

    add 'transform' flag to parse the raw gates for debug purpose


Commit id: 3b0338c9c572013157338d697ca5b70b4a4a717c

    convert asinh from c to R API

Revision: 101226
Author: s.arora
Date: 2015-03-26T18:33:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/data/biocViewsVocab.rda
Modified  /trunk/madman/Rpacks/biocViews/inst/dot/biocViewsVocab.dot
Modified  /trunk/madman/Rpacks/biocViews/inst/extdata/biocViewsVocab.sqlite
biocViews update

add CodeLinkChip to AnnotationData
Revision: 101225
Author: j.lugo
Date: 2015-03-26T18:28:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/cnvGSA/vignettes/cnvGSA-vignette.Rnw
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3fb53e18c914593999346c6deb9ab146f6021d14

    Update cnvGSA-vignette.Rnw

Revision: 101224
Author: j.lugo
Date: 2015-03-26T18:16:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/cnvGSA/inst/doc/cnvGSAUsersGuide.pdf
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 604dc0dc2db0ff49d3928535c2ee716ed8d73fbf

    Updated User Guide

Revision: 101222
Author: d.tenenbaum
Date: 2015-03-26T17:26:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioc_3.1.manifest
reinstate ontoCAT; java api will be kept alive a little longer
Revision: 101221
Author: hpages
Date: 2015-03-26T17:04:34+00:00
Paths:
Added  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau8-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/ForgeAll.R
add seed file for bosTau8 genome
Revision: 101220
Author: j.hester
Date: 2015-03-26T17:04:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_SummarizedExperiment-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/SummarizedExperiment-class.Rd
Add GRange data to ExpressionSet featureData

When SummarizedExperiment objects are coerced to ExpressionSets.
Revision: 101218
Author: atarca
Date: 2015-03-26T15:40:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/SPIA/R/spia.R
Fix a bug that occurring when plots=TRUE  and due to constant values of perturbation accumulations that were plotted using density.
Revision: 101217
Author: atarca
Date: 2015-03-26T15:26:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/PADOG/DESCRIPTION
Modified  /trunk/madman/Rpacks/PADOG/NAMESPACE
Modified  /trunk/madman/Rpacks/PADOG/R/compPADOG.R
Modified  /trunk/madman/Rpacks/PADOG/R/filteranot.R
Modified  /trunk/madman/Rpacks/PADOG/R/padog.R
Modified  /trunk/madman/Rpacks/PADOG/man/compPADOG.rd
Modified  /trunk/madman/Rpacks/PADOG/man/padog.Rd
Modified  /trunk/madman/Rpacks/PADOG/vignettes/PADOG.Rnw
Added functionality to use multiple cores in computing pathway significance p-values in the padog function and compPADOG.R.
Revision: 101215
Author: mtmorgan
Date: 2015-03-26T13:44:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biobase/inst/CITATION
Modified  /trunk/madman/Rpacks/BiocGenerics/inst/CITATION
citation needs entry="Article"
Revision: 101214
Author: w.wheeler
Date: 2015-03-26T13:30:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/CGEN/DESCRIPTION
Update description file
Revision: 101212
Author: n.karp
Date: 2015-03-26T13:04:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/PhenStat/DESCRIPTION
Modified  /trunk/madman/Rpacks/PhenStat/NAMESPACE
Modified  /trunk/madman/Rpacks/PhenStat/NOTICE
Modified  /trunk/madman/Rpacks/PhenStat/R/FETFramework.R
Added  /trunk/madman/Rpacks/PhenStat/R/LogisticFramework.R
Modified  /trunk/madman/Rpacks/PhenStat/R/MMFramework.R
Modified  /trunk/madman/Rpacks/PhenStat/R/PhenList.R
Modified  /trunk/madman/Rpacks/PhenStat/R/RRFramework.R
Modified  /trunk/madman/Rpacks/PhenStat/R/TFFramework.R
Modified  /trunk/madman/Rpacks/PhenStat/R/classes.R
Modified  /trunk/madman/Rpacks/PhenStat/R/classification.R
Modified  /trunk/madman/Rpacks/PhenStat/R/diagnostictest.R
Modified  /trunk/madman/Rpacks/PhenStat/R/graphsDataset.R
Modified  /trunk/madman/Rpacks/PhenStat/R/graphsResults.R
Modified  /trunk/madman/Rpacks/PhenStat/R/summaryOutput.R
Modified  /trunk/madman/Rpacks/PhenStat/R/testDataset.R
Added  /trunk/madman/Rpacks/PhenStat/R/transformation.R
Modified  /trunk/madman/Rpacks/PhenStat/R/vectorOutput.R
Modified  /trunk/madman/Rpacks/PhenStat/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/PhenStat/inst/extdata/testLR.csv
Modified  /trunk/madman/Rpacks/PhenStat/inst/unitTests/unitTests.R
Added  /trunk/madman/Rpacks/PhenStat/man/LRDataset.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/PhenList-class.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/PhenTestResult-class.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/analysedDataset.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/analysedSubset.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/analysisResults.Rd
Deleted  /trunk/madman/Rpacks/PhenStat/man/asmatrix.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/batchIn.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/boxplotSexGenotypeBatchAdjusted.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/comparison.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/dataset.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/determiningLambda.Rd
Deleted  /trunk/madman/Rpacks/PhenStat/man/dimnames.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/finalLRModel.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/finalTFModel.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/formulaDeterminingLambda.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getColumn.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getColumnBatchAdjusted.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getColumnView.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getCountMatrices.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getDataset.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getGenotypeEffect.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getMatrix.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getPercentageMatrix.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getStat.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getVariable.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/getVariables.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/hemiGenotype.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/htest-class.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/htestPhenStat-class.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/matrixCount.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/method.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/methodText.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/modelFormula.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/modelFormulaLR.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/multipleBatches.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/noSexes.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/parameters.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/parserOutputSummary.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/parserOutputSummaryLR.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/parserOutputTFSummary.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/printLROutput.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/pvalue.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/refGenotype.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/reverseTransformValues.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/setBatch.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/setGenotype.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/setMissingValue.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/setSex.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/setWeight.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/startLRModel.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/startModel.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/startTFModel.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/subsetText.Rd
Modified  /trunk/madman/Rpacks/PhenStat/man/testDataset.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/testFinalLRModel.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/testGenotype.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/transformValues.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/transformation.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/transformationText.Rd
Added  /trunk/madman/Rpacks/PhenStat/man/weightIn.Rd
Modified  /trunk/madman/Rpacks/PhenStat/vignettes/PhenStat.Rnw
new verstion of PhenStat
Revision: 101211
Author: r.cavalcante
Date: 2015-03-26T12:31:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich.Rnw
Add new ldefs to NEWS and detailed descriptions to vignette
Revision: 101209
Author: sdavis2
Date: 2015-03-26T11:35:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0dc7e8177e36bfa97c72d940702d4f9e13ee3f24

    Revert "sudo: false for container-based travis builds"

    This reverts commit e1a96ff19689fdc8ab1c734989cb61237f23c2e5.

Revision: 101208
Author: sdavis2
Date: 2015-03-26T11:25:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: e1a96ff19689fdc8ab1c734989cb61237f23c2e5

    sudo: false for container-based travis builds

Revision: 101207
Author: sdavis2
Date: 2015-03-26T11:09:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4fd62942960e1337301ccff27e46a614e2cff54c

    Switch to using bioc_install in .travis.yml

Revision: 101206
Author: g.yu
Date: 2015-03-26T11:03:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPseeker/R/plotTagMatrix.R
Modified  /trunk/madman/Rpacks/ChIPseeker/man/plotAvgProf.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 58af3148ad7362c4a7b8cde2e7cd7b9480790b87

    fix check warning

Revision: 101205
Author: sdavis2
Date: 2015-03-26T11:01:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f952303ff878e5d5cc15f78cd68017b7eb5a7977

    Trying out r-builder instead of r-travis

Revision: 101204
Author: whuber
Date: 2015-03-26T10:42:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biobase/DESCRIPTION
Modified  /trunk/madman/Rpacks/Biobase/inst/CITATION
Modified  /trunk/madman/Rpacks/BiocGenerics/DESCRIPTION
Added  /trunk/madman/Rpacks/BiocGenerics/inst/CITATION
Updated (Biobase) and added (BiocGenerics) the CITATION file, which now lists the 2015 paper in Nature Methods.

Revision: 101203
Author: h.froehlich
Date: 2015-03-26T10:24:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOSim/DESCRIPTION
Modified  /trunk/madman/Rpacks/GOSim/NAMESPACE
Modified  /trunk/madman/Rpacks/GOSim/R/geneSimilarity.R
Modified  /trunk/madman/Rpacks/GOSim/R/manifold_embedding.R
Modified  /trunk/madman/Rpacks/GOSim/man/getGeneSimPrototypes.Rd
Modified  /trunk/madman/Rpacks/GOSim/src/OAWrapper.cpp
Modified  /trunk/madman/Rpacks/GOSim/vignettes/GOSim.Rnw
added donttests for speed-up of check; fulfilled requirements and recommendations of BiocCheck
Revision: 101201
Author: fhahne
Date: 2015-03-26T09:48:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/Gviz/DESCRIPTION
Modified  /trunk/madman/Rpacks/Gviz/R/AllClasses.R
Modified  /trunk/madman/Rpacks/Gviz/R/Gviz-methods.R
fixing a bug in the Ideogram track when band information is NA
Revision: 101200
Author: g.yu
Date: 2015-03-26T08:59:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPseeker/NAMESPACE
Modified  /trunk/madman/Rpacks/ChIPseeker/NEWS
Modified  /trunk/madman/Rpacks/ChIPseeker/man/plotAvgProf.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 377c44322bb74a6eeacc3c0b0d10161d09a2bd04

    update docs

Revision: 101199
Author: g.yu
Date: 2015-03-26T08:38:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/R/plotTagMatrix.R
Modified  /trunk/madman/Rpacks/ChIPseeker/R/utilities.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 8c3d262af393b100253688acdf2bdf91ef116994

    Merge pull request #4 from Puriney/master

    Confidence Interval Estimation by using bootstrapping

Commit id: 6c9035e2c6c32338cf2378972509acf1d14347a5

    Accomplished. adding confidence interval feature into function plotAvgProf


Commit id: f8f2f8d71ccf152b09bed8a8d8f9036cdc0004dc

    Set up general structure for ploting confidential interval for TSS-coverage-plot

Revision: 101198
Author: g.yu
Date: 2015-03-26T03:32:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/R/bitr.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f1d996789ff3ff0800fbbe36dd825f0162aa613e

    update warning msg of bitr

Revision: 101197
Author: stvjc
Date: 2015-03-26T03:00:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/NAMESPACE
Modified  /trunk/madman/Rpacks/gQTLstats/R/cisAssocPlus.R
as prep.cisAssocNB for temp evaluation
Revision: 101196
Author: sdavis2
Date: 2015-03-26T01:26:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/NAMESPACE
Modified  /trunk/madman/Rpacks/GEOquery/vignettes/GEOquery.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6872fbd74ba8b3b78941c51ccb3f62d2fb252861

    Added queryGEO to exports


Commit id: 0a198e86c02e3eab795ead37e9c17216543ccbf8

    Changed GEO home page link

Revision: 101195
Author: r.tautenhahn
Date: 2015-03-26T01:14:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/xcms/DESCRIPTION
Steffen is taking over maintenance of the XCMS package. Thanks Steffen !!!
Revision: 101194
Author: sdavis2
Date: 2015-03-26T01:09:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/DESCRIPTION
Modified  /trunk/madman/Rpacks/GEOquery/NAMESPACE
Added  /trunk/madman/Rpacks/GEOquery/R/queryGEO.R
Added  /trunk/madman/Rpacks/GEOquery/inst/NEWS
Added  /trunk/madman/Rpacks/GEOquery/man/queryGEO.Rd
Modified  /trunk/madman/Rpacks/GEOquery/vignettes/GEOquery.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: fb8bf6d10582fd8b9a4c2a2ebe7d49cbe8ebdcc3

    Added a suggested biocViews


Commit id: 422a94f54b4ede4ed251b07c1b337fa1487dff2a

    Import rentrez functions needed


Commit id: 6a9df287adc00ce0014e0e3ccc5c63b4afd59730

    Added NEWS file


Commit id: e0cd3a59d00ca26d75e9bd378fb4defd16ce8416

    Clean up queryGEO docs


Commit id: 11e43754fd25571b8ef78abd17673e0416db3653

    Changes and additions (queryGEO, basically) to vignette


Commit id: 794de2dc3e97dc5f355a645fc6670ac33d6986ff

    Fixed list handling in queryGEO


Commit id: 5048861cce463587e121bd2f3cfe7affb0954ff6

    Rudimentary support for querying GEO metadata using rentrez

Revision: 101192
Author: hpages
Date: 2015-03-25T23:24:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/man/organism_species.Rd
add \alias{organism_species}
Revision: 101191
Author: hpages
Date: 2015-03-25T23:24:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/annotate/man/chromLocation-class.Rd
Add \alias{chromLocation} to make it easier for the user to find the man page
for chromLocation objects. This will also make \link[annotate]{chromLocation}
(from the organism_species man page in BiocGenerics) a valid link.
Revision: 101190
Author: m.lawrence
Date: 2015-03-25T23:20:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/NAMESPACE
import seqinfo and seqlengths from GenomeInfoDb
Revision: 101187
Author: hpages
Date: 2015-03-25T22:34:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromBiomart.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/utils.R
Some tweaks and fixes to makeTxDbFromBiomart():

- Drop transcripts with UTR anomalies with a warning instead of failing. We've
  started to see these hopeless transcripts with the release 79 of Ensembl in
  the dmelanogaster_gene_ensembl dataset (based on FlyBase r6.02 / FB2014_05,
  ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.02_FB2014_05/).
  With this change, the user can still make a TxDb for
  dmelanogaster_gene_ensembl but some transcripts (9 with Ensembl 79) will be
  dropped with a warning.

- BioMart data anomaly warnings and errors now show the first 3 transcripts
  instead of 6.

- Fix issue causing the download of 'chrominfo' data frame to fail when
  querying the primary Ensembl mart (with host="ensembl.org" and
  biomart="ENSEMBL_MART_ENSEMBL").
Revision: 101186
Author: s.arora
Date: 2015-03-25T22:20:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Deleted  /trunk/madman/Rpacks/AnnotationHubData/R/UCSCTrackImport-utils.R
Deleted  /trunk/madman/Rpacks/AnnotationHubData/R/UCSCTrackImportPreparer-class.R
Deleted  /trunk/madman/Rpacks/AnnotationHubData/R/importFastaFiles.R
Added  /trunk/madman/Rpacks/AnnotationHubData/R/makeUCSCTracks.R
Deleted  /trunk/madman/Rpacks/AnnotationHubData/R/trackToGRangesRecipe.R
code update

recipe update for Tracks recipe
- add code for justRunUnitTest to quickly test the recipe
- remove SourceFile,RDataVersion (Redundant field)
- add following field : Location_prefix, DisptachClass, SourceType

- file organization:
a) trackToGRangesRecipe.R has only 1 function - moved to UCSCTrackImportPreparer-class.R
b) UCSCTrackImport-utils.R  all functions moved to UCSCTrackImportPreparer-class.R
c) importFastaFiles.R  contains functions which have are no longer needed
d) UCSCTrackImportPreparer-class.R  is renamed to makeUCSCTracks.R
Revision: 101185
Author: s.arora
Date: 2015-03-25T22:10:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/webAccessFunctions.R
 code update

- fix tryCatch loop

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