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Revision: 96021
Author: hpages
Date: 2014-10-25T00:44:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/Seqinfo-class.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/Seqinfo-class.Rd
genome() setter was too paranoid when checking the supplied value and was
causing the 'genome(x) <- genome(y)' idiom to fail most of the time. Relaxed
its logic a tiny bit (without sacrificing safety) so now this idiom should
almost always work.
Revision: 96020
Author: t.backman
Date: 2014-10-24T23:46:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioassayR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 72490f2f208e5179c726f0da36d018cc3747b86d

    removed DBI version number

Committed by: TylerBackman
Author Name: TylerBackman
Commit date: 2014-10-24 16:46:09 -0700
Author date: 2014-10-24 16:46:09 -0700
Revision: 96019
Author: t.backman
Date: 2014-10-24T23:40:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioassayR/DESCRIPTION
Modified  /trunk/madman/Rpacks/bioassayR/R/BioassayDB-accessors.R
Modified  /trunk/madman/Rpacks/bioassayR/R/loadingData.R
Modified  /trunk/madman/Rpacks/bioassayR/R/queries.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 4a4d5c71f64bce5510b026fd2f10e3289121ebe2

    rolled back RSQLite 1.0.0 changes again- why did this unhappen?

Committed by: TylerBackman
Author Name: TylerBackman
Commit date: 2014-10-24 16:40:05 -0700
Author date: 2014-10-24 16:40:05 -0700
Revision: 96014
Author: l.goldstein
Date: 2014-10-24T22:32:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/SGSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/SGSeq/R/data.R
Modified  /trunk/madman/Rpacks/SGSeq/man/gr.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/sgf.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/sgfc.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/si.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/txf.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/txv.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/txvc.Rd
tagged documentation for example data as internal
Revision: 96012
Author: s.aibar
Date: 2014-10-24T22:20:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/DESCRIPTION
Modified  /trunk/madman/Rpacks/FGNet/R/plotKegg.R
plotKegg: trycatch in download
Revision: 96006
Author: hpages
Date: 2014-10-24T21:25:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/NAMESPACE
Deleted  /trunk/madman/Rpacks/BSgenome/R/ExtraSNPlocs-class.R
Added  /trunk/madman/Rpacks/BSgenome/R/XtraSNPlocs-class.R
- Rename ExtraSNPlocs class -> XtraSNPlocs.
- Add snpsBySeqname() and snpsById() generics with methods only for XtraSNPlocs
  objects for now ("snpsById" method not fully implemented yet).
- Remove "snplocs" method for XtraSNPlocs objects for now.
Revision: 96005
Author: hpages
Date: 2014-10-24T21:18:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/OnDiskLongTable-class.R
- rename saveAsOnDiskLongTable() 'batch.label' arg -> 'batch_label'
- add 'with.batch_label' and 'as.data.frame' arg to getDataFromOnDiskLongTable()
Revision: 96000
Author: s.arora
Date: 2014-10-24T19:31:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/seqlevelsStyle.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/inst/unitTests/test_seqlevels-wrappers.R
code update

- bug pointed out by Leo
- bug: the style which have a [.] in them were being truncated incorrectly.
- soln : use gsub and sub and get rid of strsplit()
- add unit tests for .guessSpeciesStyle()
Revision: 95999
Author: c.warden
Date: 2014-10-24T19:22:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/COHCAP/CHANGES
Modified  /trunk/madman/Rpacks/COHCAP/DESCRIPTION
Updating code from previous version
Revision: 95997
Author: v.obenchain
Date: 2014-10-24T19:01:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/vignettes/GenomicFiles.Rnw
remove duplicate vignette section label
Revision: 95995
Author: t.backman
Date: 2014-10-24T18:30:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioassayR/DESCRIPTION
Added  /trunk/madman/Rpacks/bioassayR/R/bioassaySet-accessors.R
Modified  /trunk/madman/Rpacks/bioassayR/man/bioassaySet-class.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 0 commit.

Commit information:


Revision: 95993
Author: s.arora
Date: 2014-10-24T17:44:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Added  /trunk/madman/Rpacks/GenomeInfoDb/inst/extdata/dataFiles/rattus_norvegicus.txt
code update

- adding support for Rats in GenomeInfoDb. 
Revision: 95992
Author: hpages
Date: 2014-10-24T17:40:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/ExtraSNPlocs-class.R
oops, please read snplocs() instead of snpcount() in previous commit message
Revision: 95991
Author: hpages
Date: 2014-10-24T17:38:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/ExtraSNPlocs-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/SNPlocs-class.R
rename snpcount() arg 'seqname' -> 'seqnames'
Revision: 95989
Author: s.aibar
Date: 2014-10-24T17:20:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/geNetClassifier/vignettes/geNetClassifier-vignette.Rnw
Vignette update
Revision: 95986
Author: s.aibar
Date: 2014-10-24T16:59:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/DESCRIPTION
Vignette update
Revision: 95985
Author: s.aibar
Date: 2014-10-24T16:59:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/vignettes/FGNet.Rmd
Vignette update
Revision: 95981
Author: m.love
Date: 2014-10-24T16:03:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
fixing the sample distance problem: thx Jesse Rowley
Revision: 95980
Author: a.luna
Date: 2014-10-24T15:38:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/paxtoolsr
Modified  /trunk/madman/Rpacks/paxtoolsr/DESCRIPTION
Modified  /trunk/madman/Rpacks/paxtoolsr/NAMESPACE
Modified  /trunk/madman/Rpacks/paxtoolsr/NEWS
Modified  /trunk/madman/Rpacks/paxtoolsr/R/pathwayCommons.R
Modified  /trunk/madman/Rpacks/paxtoolsr/R/paxtools.R
Modified  /trunk/madman/Rpacks/paxtoolsr/R/paxtoolsr.R
Added  /trunk/madman/Rpacks/paxtoolsr/inst/extdata/test_gsea.gmt
Added  /trunk/madman/Rpacks/paxtoolsr/inst/extdata/test_sifnx.txt
Modified  /trunk/madman/Rpacks/paxtoolsr/inst/tests/test_pathwayCommons.R
Modified  /trunk/madman/Rpacks/paxtoolsr/inst/tests/test_paxtools.R
Modified  /trunk/madman/Rpacks/paxtoolsr/man/downloadPc.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/fetch.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/fromPsimi.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/getNeighbors.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/getPc.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/graphPc.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/idMapping.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/integrateBiopax.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/mergeBiopax.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/pcDirections.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/pcFormats.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/pcGraphQueries.Rd
Added  /trunk/madman/Rpacks/paxtoolsr/man/readGmt.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/searchPc.Rd
Added  /trunk/madman/Rpacks/paxtoolsr/man/splitSifnx.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/summarize.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/toGSEA.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/toLevel3.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/toSBGN.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/toSif.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/toSifnx.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/topPathways.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/traverse.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/man/validate.Rd
Modified  /trunk/madman/Rpacks/paxtoolsr/vignettes/using_paxtoolsr.Rmd
Transitioned to Pathway Commons Version 5 (PC2 v5)
Changed downloadPc to download from PC2 v5
Changed code to validate Pathway Commons webservice requests
Added table of contents to vignette
Added description for traverse() in vignette
Changed R dependency to 3.1.1 to match Bioconductor 3
Added function to download a single file extended SIF, splitSifnx
Added the ability to download GMT in downloadPc
Added function to read GMT files
Added tests for new functions
Revision: 95979
Author: v.obenchain
Date: 2014-10-24T14:38:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/man/reduceByYield.Rd
Modified  /trunk/madman/Rpacks/GenomicFiles/vignettes/GenomicFiles.Rnw
edits to documentation
Revision: 95973
Author: p.pyl
Date: 2014-10-24T10:01:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/h5vc/DESCRIPTION
Modified  /trunk/madman/Rpacks/h5vc/R/prepareTallyFile.R
Modified  /trunk/madman/Rpacks/h5vc/man/tallyBAM.Rd
Modified  /trunk/madman/Rpacks/h5vc/src/tallyBAM.cpp
reworked tallyBAM
Revision: 95972
Author: m.boenn
Date: 2014-10-24T08:44:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/geecc/DESCRIPTION
Changed GO2list and KEGG2list
Revision: 95970
Author: hpages
Date: 2014-10-24T08:23:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/ExtraSNPlocs-class.R
implement "snpcount" and "snplocs" methods for ExtraSNPlocs objects
Revision: 95967
Author: v.obenchain
Date: 2014-10-24T03:15:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/R/MulticoreParam-class.R
add check to bpiterate() for Windows
Revision: 95965
Author: a.lerch
Date: 2014-10-24T00:51:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/QuasR
Modified  /trunk/madman/Rpacks/QuasR/R/qQCReport.R
Bugfix 'need finite 'ylim' values'. If read1 and read2 have different length, the function max returns NaN. Fix with option na.rm=T.
Revision: 95962
Author: d.strbenac
Date: 2014-10-24T00:00:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/mixmodels.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/naiveBayesKernel.R
Handling of multiple return lists when minDifference is a single number is fixed.
Revision: 95961
Author: l.collado-torres
Date: 2014-10-23T23:50:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/derfinder/R/extendedMapSeqlevels.R
Modified  /trunk/madman/Rpacks/derfinder/README.md
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_misc.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 2418a438b2cbb7c869c3da50fdacfefa45f7076c

    v1.1.6 -- Updated to match changes in GenomeInfoDb 1.3.3

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-23 19:50:49 -0400
Author date: 2014-10-23 19:50:49 -0400
Revision: 95960
Author: n.hayden
Date: 2014-10-23T23:42:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/h5vc/DESCRIPTION
Modified  /trunk/madman/Rpacks/h5vc/vignettes/h5vc.tour.Rmd
copy patch from release to fix vignette header
Revision: 95957
Author: n.hayden
Date: 2014-10-23T23:21:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCore/DESCRIPTION
version bump
Revision: 95955
Author: mtmorgan
Date: 2014-10-23T22:59:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/NEWS
update NEWS and DESCRIPTION
Revision: 95954
Author: mtmorgan
Date: 2014-10-23T22:59:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/src/bam_data.c
Modified  /trunk/madman/Rpacks/Rsamtools/src/bam_data.h
grow cigar buffer when needed
Revision: 95953
Author: mtmorgan
Date: 2014-10-23T22:58:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/src/io_sam.c
Modified  /trunk/madman/Rpacks/Rsamtools/src/scan_bam_data.c
Modified  /trunk/madman/Rpacks/Rsamtools/src/utilities.c
Modified  /trunk/madman/Rpacks/Rsamtools/src/utilities.h
handle BAM parse errors better

- Realloc() fails when allocating 0 bytes
- don't try to finalize to R when parse error occurs
Revision: 95952
Author: mtmorgan
Date: 2014-10-23T22:56:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/src/pbuffer_wrapper.h
clean up function exposure

- code needs to be exposed in C and C++, not in C++ w/ C linkage
Revision: 95951
Author: hpages
Date: 2014-10-23T22:50:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
version bump
Revision: 95949
Author: n.hayden
Date: 2014-10-23T22:24:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCore/src/Hyperlog.cpp
Modified  /trunk/madman/Rpacks/flowCore/src/Logicle.cpp
use operator delete[] on taylor member of (hyperlog|logicle)_params
structs in Hyperlog/Logicle destructors
Revision: 95947
Author: v.obenchain
Date: 2014-10-23T21:09:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-readVcf.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_readVcf-methods.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/readVcf-methods.Rd
update unit tests for 'genome' as Seqinfo
Revision: 95943
Author: m.chae
Date: 2014-10-23T20:31:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/groHMM/DESCRIPTION
Modified  /trunk/madman/Rpacks/groHMM/inst/CITATION
Fixed CITATION
Revision: 95942
Author: m.chae
Date: 2014-10-23T20:24:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/groHMM/DESCRIPTION
Modified  /trunk/madman/Rpacks/groHMM/inst/CITATION
Updated DESCRIOPTION and CITATION
Revision: 95940
Author: v.obenchain
Date: 2014-10-23T19:17:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-readVcf.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/readVcf-methods.Rd
fix bug in readVcf() when 'genome' is a Seqinfo object
Revision: 95939
Author: t.mayo
Date: 2014-10-23T19:09:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/M3D/DESCRIPTION
Modified  /trunk/madman/Rpacks/M3D/NEWS
Modified  /trunk/madman/Rpacks/M3D/R/pvals.R
Modified  /trunk/madman/Rpacks/M3D/inst/unitTests/test_M3Dpackage.R
Modified  /trunk/madman/Rpacks/M3D/vignettes/M3D_vignette.Rnw
Updated pvals function to model the null
Revision: 95935
Author: a.oles
Date: 2014-10-23T16:34:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBImage/R/Image.R
Modified  /trunk/madman/Rpacks/EBImage/R/display.R
Modified  /trunk/madman/Rpacks/EBImage/man/Image.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/bwlabel.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/channel.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/colorLabels.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/combine.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/computeFeatures.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/display.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/distmap.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/drawCircle.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/fillHull.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/filter2.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/floodFill.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/gblur.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/io.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/localCurvature.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/medianFilter.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/morphology.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/normalize.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/ocontour.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/otsu.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/paintObjects.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/propagate.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/rmObjects.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/spatial.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/stackObjects.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/thresh.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/tile.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/transpose.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/watershed.Rd
version 4.9.1
- the default display method depends on interactive()
- account for arbitrary number of color channels in 'as.nativeRaster'
- fill missing color channels when displaying in browser
- 'combine': only images of the same color mode can be combined
Revision: 95934
Author: p.stempor
Date: 2014-10-23T16:27:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: d4128926ccc53e6e6a0ce85e2a4e167c500804ed

    SeqPlots version displayed in GUI and updated PDF link

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-23 17:26:36 +0100
Author date: 2014-10-23 17:26:36 +0100
Revision: 95933
Author: p.stempor
Date: 2014-10-23T15:56:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Modified  /trunk/madman/Rpacks/seqplots/R/int_getSF.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 195077c5e1285e7d5c5b0a722054cf7187d576af

    version bump - 1.1.4

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-23 16:54:56 +0100
Author date: 2014-10-23 16:54:56 +0100

Commit id: 10cd672d0461d1be2c45fdf28add1862396eae11

    fixed error in approx function when genomic feature width equals 1

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-23 16:54:22 +0100
Author date: 2014-10-23 16:54:22 +0100
Revision: 95931
Author: p.stempor
Date: 2014-10-23T15:31:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/R/int_getSF.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: d449f97888f7e47b838b6a5b92b45caa27306e9c

    vectorized implementation of getSF, big speed-up in motif plots

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-23 16:29:59 +0100
Author date: 2014-10-23 16:29:59 +0100
Revision: 95929
Author: m.stadler
Date: 2014-10-23T12:49:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/QuasR/DESCRIPTION
Modified  /trunk/madman/Rpacks/QuasR/inst/unitTests/help_function.R
Modified  /trunk/madman/Rpacks/QuasR/man/qCount.Rd
Modified  /trunk/madman/Rpacks/QuasR/vignettes/QuasR.Rnw
v1.7.2: replace depricated GenomicFeatures::makeTranscriptTbFromGFF by makeTxDbFromGFF
Revision: 95927
Author: r.nicolle
Date: 2014-10-23T12:20:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/CoRegNet/DESCRIPTION
Added  /trunk/madman/Rpacks/CoRegNet/vignettes/.Rhistory
Modified  /trunk/madman/Rpacks/CoRegNet/vignettes/CoRegNet.Rnw
setting up git-svn bridge
Revision: 95924
Author: d.strbenac
Date: 2014-10-23T07:30:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/errorMap.R
Legends are aligned better in errorMap.
Revision: 95922
Author: d.strbenac
Date: 2014-10-23T07:01:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/NAMESPACE
Modified  /trunk/madman/Rpacks/ClassifyR/R/classifyInterface.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/edgeRselection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/errorMap.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/leveneSelection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/likelihoodRatioSelection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/limmaSelection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/mixmodels.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/naiveBayesKernel.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/runTest.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/runTests.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/utilities.R
Modified  /trunk/madman/Rpacks/ClassifyR/man/errorMap.Rd
 - Bugs in multiple functions are fixed when multiple return values are returned from the predictor.
- errorMap has lots more customisation, including suppression of axes labels, legends. It also allows the classes to hae errors coloured differently.

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