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Revision: 76777
Author: a.honkela
Date: Tue, 21 May 2013 12:13:19 GMT
Paths:
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
tigre 1.15.1: bug fixes to non-cascade model (identical to tigre 1.14.1)
Revision: 76775
Author: r.stojnic
Date: Tue, 21 May 2013 10:58:04 GMT
Paths:
Modified  /trunk/madman/Rpacks/PWMEnrich/R/MotifEnrichmentResults-methods.R
Fixed a typo
Revision: 76772
Author: radivot
Date: Tue, 21 May 2013 09:50:44 GMT
Paths:
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
fixed sod example. Source of integration instability was my clipping of negative concentrations to zero. So I fixed simulate to no longer do this.
Revision: 76771
Author: t.yin
Date: Tue, 21 May 2013 05:47:50 GMT
Paths:
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
fix tracks bugs for labeling and remove Grob class subclass, this may be confusing
Revision: 76770
Author: t.yin
Date: Tue, 21 May 2013 03:56:42 GMT
Paths:
Modified  /trunk/madman/Rpacks/biovizBase/R/addStepping-method.R
Modified  /trunk/madman/Rpacks/biovizBase/man/addStepping-method.Rd
add fix arguments
Revision: 76768
Author: h.bengtsson
Date: Tue, 21 May 2013 02:08:09 GMT
Paths:
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
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.
Revision: 76766
Author: h.bengtsson
Date: Tue, 21 May 2013 01:05:52 GMT
Paths:
Modified  /trunk/madman/Rpacks/aroma.light/man/callNaiveGenotypes.numeric.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/wpca.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeTumorBoost.numeric.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/fitNaiveGenotypes.numeric.Rd
Modified  /trunk/madman/Rpacks/aroma.light/DESCRIPTION
Modified  /trunk/madman/Rpacks/aroma.light/man/plotXYCurve.numeric.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/iwpca.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotMvsAPairs.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotXYCurve.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotMvsA.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/fitIWPCA.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/calibrateMultiscan.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/inst/NEWS
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeCurveFit.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/fitXYCurve.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeAffine.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeQuantileRank.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotMvsMPairs.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/robustSmoothSpline.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/likelihood.smooth.spline.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeFragmentLength.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotDensity.list.Rd
Version: 1.31.2 [2013-05-20]
o Same updates as in v1.30.2.

Version: 1.30.2 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
Revision: 76765
Author: y.liao
Date: Mon, 20 May 2013 23:48:58 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor improvement of featureCounts
Revision: 76764
Author: t.yin
Date: Mon, 20 May 2013 18:51:14 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/man/tracks.Rd
Modified  /trunk/madman/Rpacks/ggbio/R/ideogram.R
Modified  /trunk/madman/Rpacks/ggbio/R/tracks.R
Modified  /trunk/madman/Rpacks/ggbio/R/GGbio-class.R
Modified  /trunk/madman/Rpacks/ggbio/NAMESPACE
Modified  /trunk/madman/Rpacks/ggbio/R/Tracked-class.R
Modified  /trunk/madman/Rpacks/ggbio/R/Plot-class.R
fix major broken issues of tracks function, need to support old accessor API too I guess though
Revision: 76761
Author: j.hon
Date: Mon, 20 May 2013 17:59:40 GMT
Paths:
Modified  /trunk/madman/Rpacks/triplex/man/triplex.3D.Rd
Modified  /trunk/madman/Rpacks/triplex/NAMESPACE
Modified  /trunk/madman/Rpacks/triplex/R/triplex.3D.R
Modified  /trunk/madman/Rpacks/triplex/DESCRIPTION
rgl moved from Depends into Suggests
Revision: 76760
Author: radivot
Date: Mon, 20 May 2013 17:48:31 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/inst/models/sod.R
Added  /trunk/madman/Rpacks/SBMLR/inst/models/sodNatural.R
added sodNatural.R, but I can't seem to make it work
Revision: 76759
Author: j.muller
Date: Mon, 20 May 2013 17:36:52 GMT
Paths:
Modified  /trunk/madman/Rpacks/TransView/NEWS
Modified  /trunk/madman/Rpacks/TransView/man/meltPeak.Rd
Modified  /trunk/madman/Rpacks/TransView/DESCRIPTION
Modified  /trunk/madman/Rpacks/TransView/R/TransView_tools.R
Modified  /trunk/madman/Rpacks/TransView/man/TransView-package.Rd
CHANGES IN VERSION 1.5.3
------------------------

NEW FEATURES

    o meltPeak can return loess smoothed scores.
Revision: 76758
Author: l.chavez
Date: Mon, 20 May 2013 17:20:23 GMT
Paths:
Modified  /trunk/madman/Rpacks/MEDIPS/DESCRIPTION
Modified  /trunk/madman/Rpacks/MEDIPS/inst/doc/MEDIPS.Rnw
Manual distance=1 update
Revision: 76757
Author: p.haverty
Date: Mon, 20 May 2013 17:13:02 GMT
Paths:
Modified  /trunk/madman/Rpacks/genoset/man/segs2RleDataFrame.Rd
Modified  /trunk/madman/Rpacks/genoset/NAMESPACE
Modified  /trunk/madman/Rpacks/genoset/man/segs2RangedData.Rd
Modified  /trunk/madman/Rpacks/genoset/R/segments.R
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Fixed roxygen2 segments family see also
Revision: 76756
Author: p.haverty
Date: Mon, 20 May 2013 17:10:14 GMT
Paths:
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Now importing width from GenomicRanges
Revision: 76755
Author: p.haverty
Date: Mon, 20 May 2013 16:34:38 GMT
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
IRanges now both Depends and Imports
Revision: 76754
Author: t.yates
Date: Mon, 20 May 2013 15:57:12 GMT
Paths:
Modified  /trunk/madman/Rpacks/annmap/DESCRIPTION
Modified  /trunk/madman/Rpacks/annmap/inst/unitTests/runit.coords.R
Modified  /trunk/madman/Rpacks/annmap/R/coords.R
Modified  /trunk/madman/Rpacks/annmap/inst/NEWS.Rd
Fix for transcriptCoordsToGenome

* ANNMAP112:
  Up to v1.3.1
  Added NEWS of fix
  Fix for ANNMAP-112 use as.integer rather than as.numeric
  Unit test for ANNMAP-112 bug with transcript/protein CoordsToGenome
Revision: 76753
Author: y.liao
Date: Mon, 20 May 2013 15:55:12 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor improvement of featureCounts
Revision: 76751
Author: radivot
Date: Mon, 20 May 2013 12:01:57 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/man/simulate.Rd
Added  /trunk/madman/Rpacks/SBMLR/inst/models/curtoNatural.R
Added  /trunk/madman/Rpacks/SBMLR/inst/models/sod.xml
Added  /trunk/madman/Rpacks/SBMLR/inst/models/sod.R
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/summary.SBML.r
Modified  /trunk/madman/Rpacks/SBMLR/NEWS
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBML.r
added SOD model and curtoNatural.R to models. Removed need for reversible flag in SBMLR model files.
Revision: 76750
Author: j.hon
Date: Mon, 20 May 2013 09:52:05 GMT
Paths:
Modified  /trunk/madman/Rpacks/triplex/DESCRIPTION
Stric rgl dependency
Revision: 76748
Author: y.liao
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/sambam-file.h
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
Modified  /trunk/madman/Rpacks/Rsubread/src/sambam-file.c
removed wrong message from featureCounts
Revision: 76747
Author: g.yu
Date: Mon, 20 May 2013 05:33:44 GMT
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Modified  /trunk/madman/Rpacks/clusterProfiler/R/utilities.R
Modified  /trunk/madman/Rpacks/clusterProfiler/R/enrichKEGG.R
enrichGO and enrichKEGG support rat organism <2013-05-20, Mon>
Revision: 76746
Author: p.murrell
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/hyperdraw/inst/doc/hyperdraw.Rnw
Modified  /trunk/madman/Rpacks/hyperdraw/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/hyperdraw/R/draw.R
add "start" option for "arrowLoc"
Revision: 76745
Author: p.murrell
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/hyperdraw/R/hypergraph.R
Modified  /trunk/madman/Rpacks/hyperdraw/inst/doc/hyperdraw.Rnw
Modified  /trunk/madman/Rpacks/hyperdraw/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/hyperdraw/R/draw.R
add "both" option for "arrowLoc";  bug fix for conversion from Hypregraph to graphBPH
Revision: 76744
Author: y.liao
Date: Sun, 19 May 2013 23:30:44 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
removed wrong message from featureCounts
Revision: 76743
Author: t.yin
Date: Sun, 19 May 2013 22:51:54 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/man/tracks.Rd
Modified  /trunk/madman/Rpacks/ggbio/DESCRIPTION
update manual of tracks
Revision: 76742
Author: t.yin
Date: Sun, 19 May 2013 22:51:33 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/tests/runTests.R
Added  /trunk/madman/Rpacks/ggbio/tests
add test folder and file
Revision: 76741
Author: t.yin
Date: Sun, 19 May 2013 22:50:35 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/inst/tests/test_grob.R
update test
Revision: 76740
Author: t.yin
Date: Sun, 19 May 2013 22:50:20 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/NAMESPACE
update NAMESPACE
Revision: 76739
Author: t.yin
Date: Sun, 19 May 2013 22:36:24 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/tracks.R
Modified  /trunk/madman/Rpacks/ggbio/R/GGbio-class.R
Modified  /trunk/madman/Rpacks/ggbio/R/utils.R
tweak and move around functions
Revision: 76738
Author: t.yin
Date: Sun, 19 May 2013 22:34:38 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/ggplot-method.R
remove ggplot,Any
Revision: 76737
Author: t.yin
Date: Sun, 19 May 2013 22:34:14 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/AllClasses.R
add numericORNULL
Revision: 76736
Author: t.yin
Date: Sun, 19 May 2013 22:32:02 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/plotRangesLinkedToData.R
fix a typo
Revision: 76735
Author: t.yin
Date: Sun, 19 May 2013 22:31:40 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/man/Plot-class.Rd
Added  /trunk/madman/Rpacks/ggbio/R/Plot-class.R
add Plot Class
Revision: 76734
Author: t.yin
Date: Sun, 19 May 2013 22:31:18 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/man/Grob-class.Rd
Added  /trunk/madman/Rpacks/ggbio/R/Grob-class.R
add Grob class
Revision: 76733
Author: t.yin
Date: Sun, 19 May 2013 21:28:40 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/inst/tests/test_grob.R
Added  /trunk/madman/Rpacks/ggbio/inst/tests
add test directory
Revision: 76732
Author: t.yin
Date: Sun, 19 May 2013 21:24:56 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/R/Cache-class.R
Added  /trunk/madman/Rpacks/ggbio/man/Cache-class.Rd
add Cache class
Revision: 76731
Author: t.yin
Date: Sun, 19 May 2013 21:24:28 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/man/Tracked-class.Rd
Added  /trunk/madman/Rpacks/ggbio/R/Tracked-class.R
add Tracked class
Revision: 76730
Author: mtmorgan
Date: Sun, 19 May 2013 12:13:41 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/R/SnapshotFunction-helpers.R
Modified  /trunk/madman/Rpacks/ShortRead/R/Snapshot.R
Modified  /trunk/madman/Rpacks/ShortRead/R/spViewPerFeature.R
Modified  /trunk/madman/Rpacks/ShortRead/man/Snapshot-class.Rd
quieten warnings from Snapshot

- use seqlevels<-
- avoid setting scales in update() -- bug in lattice??
Revision: 76728
Author: mtmorgan
Date: Sun, 19 May 2013 04:01:52 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/NEWS
DESCRIPTION and NEWS update
Revision: 76727
Author: mtmorgan
Date: Sun, 19 May 2013 02:36:24 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_trimEnds.R
Added  /trunk/madman/Rpacks/ShortRead/R/trimEnds.R
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_trimTails.R
Modified  /trunk/madman/Rpacks/ShortRead/man/trimTails.Rd
trim*,character-methods using filterFastq
Revision: 76726
Author: mtmorgan
Date: Sun, 19 May 2013 02:35:41 GMT
Paths:
Added  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_filterFastq.R
Added  /trunk/madman/Rpacks/ShortRead/man/filterFastq.Rd
Added  /trunk/madman/Rpacks/ShortRead/R/filterFastq.R
filterFastq methods
Revision: 76725
Author: mtmorgan
Date: Sat, 18 May 2013 19:19:18 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_writeFastq_test.R
Modified  /trunk/madman/Rpacks/ShortRead/R/methods-ShortReadQ.R
write 0-length fastq files
Revision: 76724
Author: mtmorgan
Date: Sat, 18 May 2013 19:16:25 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/R/methods-QualityScore.R
Modified  /trunk/madman/Rpacks/ShortRead/man/QualityScore-class.Rd
Modified  /trunk/madman/Rpacks/ShortRead/NAMESPACE
encoding,QualityScore-methods
Revision: 76723
Author: mtmorgan
Date: Sat, 18 May 2013 19:06:16 GMT
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringQuality-class.R
Modified  /trunk/madman/Rpacks/Biostrings/NAMESPACE
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringQuality-class.Rd
alphabet and encoding methods for XStringQuality
Revision: 76722
Author: hpages
Date: Sat, 18 May 2013 04:56:45 GMT
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/SplicingGraphs.Rnw
small tweaks to vignette
Revision: 76721
Author: radivot
Date: Sat, 18 May 2013 03:09:57 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/simulate.r
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/summary.SBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBML.r
got it to pass check with VV additions
Revision: 76720
Author: hpages
Date: Sat, 18 May 2013 02:01:51 GMT
Paths:
Added  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/precomputed_results/sg_with_bubbles.rda
Modified  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/precomputed_results/sg_with_reads.rda
Modified  /trunk/madman/Rpacks/SplicingGraphs/DESCRIPTION
Modified  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/SplicingGraphs.Rnw
Modified  /trunk/madman/Rpacks/SplicingGraphs/TODO
Deleted  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/precomputed_results/sg.rda
Use new RNAseqData.HeLa.bam.chr14 dataset in the vignette instead of
TBX20BamSubset.
Revision: 76719
Author: y.liao
Date: Fri, 17 May 2013 23:53:47 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor updated
Revision: 76718
Author: y.liao
Date: Fri, 17 May 2013 23:53:21 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor updated
Revision: 76717
Author: y.liao
Date: Fri, 17 May 2013 23:46:03 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor updated
Revision: 76716
Author: radivot
Date: Fri, 17 May 2013 23:33:29 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/R/simulate.r
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBML.r
Added in the rest of VV's changes, i.e. from SBMLR on github
Revision: 76715
Author: l.chavez
Date: Fri, 17 May 2013 21:55:54 GMT
Paths:
Modified  /trunk/madman/Rpacks/MEDIPS/R/MEDIPS.mergeFrames.R
Modified  /trunk/madman/Rpacks/MEDIPS/DESCRIPTION
MEDIPS.mergeFrames trim parameter
Revision: 76714
Author: p.haverty
Date: Fri, 17 May 2013 20:21:10 GMT
Paths:
Deleted  /trunk/madman/Rpacks/genoset/man/rangeSegMeanLength.Rd
Modified  /trunk/madman/Rpacks/genoset/man/rangeSegMeanLength-methods.Rd
Modified  /trunk/madman/Rpacks/genoset/inst/unitTests/test_segments.R
Modified  /trunk/madman/Rpacks/genoset/R/segments.R
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Updated tests for rangeSegMeanLength and Rd
Revision: 76713
Author: m.lawrence
Date: Fri, 17 May 2013 17:46:48 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/plotRangesLinkedToData.R
plotRangesLinkedToData now a generic, with a method for
SummarizedExperiment. Not tested at all.
Revision: 76703
Author: v.obenchain
Date: Fri, 17 May 2013 15:50:58 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/utils.R
Clean up how the default value is set for 'showHeaderLines' and 'showTailLine'.
Revision: 76702
Author: radivot
Date: Fri, 17 May 2013 15:02:04 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR
svn ignore RStudio project file added
Revision: 76701
Author: radivot
Date: Fri, 17 May 2013 15:01:03 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/inst/doc/quick-start.Rnw
Modified  /trunk/madman/Rpacks/SBMLR
Modified  /trunk/madman/Rpacks/SBMLR/man/simulate.Rd
Modified  /trunk/madman/Rpacks/SBMLR/DESCRIPTION
Modified  /trunk/madman/Rpacks/SBMLR/R/simulate.r
Modified  /trunk/madman/Rpacks/SBMLR/R/summary.SBML.r
Added  /trunk/madman/Rpacks/SBMLR/NEWS
 Vishak Venkateswaran has a branch of SBMLR up at github that I'm starting to go through. So far I added his changes to summary and simulate.
Revision: 76700
Author: m.stadler
Date: Fri, 17 May 2013 13:58:27 GMT
Paths:
Modified  /trunk/madman/Rpacks/QuasR/man/qAlign.Rd
update qAlign documentation with index storage locations
Revision: 76697
Author: r.day
Date: Fri, 17 May 2013 02:45:19 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/R/expectedUtility.R
expectedUtility:
 added guarantee parameter,
 corrected the format of the "details" block,
 put quotes around "piHat".
Revision: 76696
Author: r.day
Date: Fri, 17 May 2013 02:41:27 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/R/fit2clusters.R
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76695
Author: r.day
Date: Fri, 17 May 2013 02:39:42 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/man/expectedUtility.Rd
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76694
Author: r.day
Date: Fri, 17 May 2013 02:38:23 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/man/fit2clusters.Rd
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76693
Author: r.day
Date: Fri, 17 May 2013 02:25:35 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/R/zzz.R
Replacing .First.lib by .onLoad
Revision: 76692
Author: y.liao
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
robust featureCount load_features
Revision: 76691
Author: y.liao
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
robust featureCount load_features
Revision: 76690
Author: hpages
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/DESCRIPTION
Modified  /trunk/madman/Rpacks/SplicingGraphs/man/plotTranscripts-methods.Rd
Modified  /trunk/madman/Rpacks/SplicingGraphs/R/plotTranscripts-methods.R
Add 'max.plot.reads' arg to plotTranscripts(). Default is 200.
Revision: 76689
Author: v.obenchain
Date: Thu, 16 May 2013 23:01:42 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/utils.R
Fix bug in 'show' related to 'showHeaderLines' and 'showTailLines'.
Revision: 76684
Author: v.obenchain
Date: Thu, 16 May 2013 22:04:22 GMT
Paths:
Modified  /trunk/madman/Rpacks/ensemblVEP/R/methods-parseCSQToGRanges.R
Modified  /trunk/madman/Rpacks/ensemblVEP/DESCRIPTION
Modified  /trunk/madman/Rpacks/ensemblVEP/inst/doc/ensemblVEP.Rnw
Modified  /trunk/madman/Rpacks/ensemblVEP/man/parseCSQToGRanges.Rd
Modify 'VCFRowID' argument to parseCSQToGRanges() to handle results returned in
any order or subset.
Revision: 76679
Author: mtmorgan
Date: Thu, 16 May 2013 21:12:43 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
more efficient ref class constructor

- new empty instance, the update slots
Revision: 76678
Author: v.obenchain
Date: Thu, 16 May 2013 20:27:51 GMT
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/predictCoding-methods.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_VCF-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/locateVariants-methods.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/VCF-class.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/summarizeVariants-methods.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-scanVcf.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/getTranscriptSeqs-methods.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/doc/VariantAnnotation.Rnw
- Replace calls to keepSeqlevels() and renameSeqlevels() with seqlevels().
- Header info is accessed twice in readVcf() which resulted in a double
  (identical) warning if one was thrown. Now only a single warning is thrown.
Revision: 76677
Author: v.obenchain
Date: Thu, 16 May 2013 19:14:40 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/seqinfo.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_Seqinfo-class.R
Work on examples on 'seqinfo' man page and 'Seqinfo' unit tests.

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