Subversion Logs

This is a list of recent commits to the development branch of the Bioconductor Subversion repository.

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Revision: 117913
Author: jspidlen
Date: 2016-05-26T23:20:39+00:00
Paths:
Added  /trunk/madman/Rpacks/flowQB/man/split_in_two-methods.Rd
Some more documentation.
Revision: 117912
Author: jspidlen
Date: 2016-05-26T23:20:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/NAMESPACE
Modified  /trunk/madman/Rpacks/flowQB/R/helperFunctions.R
Added  /trunk/madman/Rpacks/flowQB/R/methods.R
Added  /trunk/madman/Rpacks/flowQB/inst/unitTests/test_split_in_two.R
More functionality and more refactoring.
Revision: 117910
Author: v.obenchain
Date: 2016-05-26T21:35:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/ExperimentHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/ExperimentHubData/vignettes/ExperimentHubData.Rmd
update vignette
Revision: 117908
Author: hpages
Date: 2016-05-26T21:11:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/R/Hits-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/subsetting-utils.R
a couple of minor tweaks
Revision: 117907
Author: hpages
Date: 2016-05-26T21:05:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
minor rephrasing
Revision: 117906
Author: jspidlen
Date: 2016-05-26T21:02:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/R/helperFunctions.R
Modified  /trunk/madman/Rpacks/flowQB/man/fitted_ellipse_gate.Rd
Fixed documentation for fitted_ellipse_gate.
Revision: 117905
Author: v.obenchain
Date: 2016-05-26T20:58:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/grasp2db/DESCRIPTION
Modified  /trunk/madman/Rpacks/grasp2db/man/grasp2db-package.Rd
fix broken select() example
Revision: 117903
Author: s.manimaran
Date: 2016-05-26T20:20:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/BatchQC/DESCRIPTION
Modified  /trunk/madman/Rpacks/BatchQC/R/batchQC.R
Modified  /trunk/madman/Rpacks/BatchQC/inst/shiny/BatchQC/server.R
Modified  /trunk/madman/Rpacks/BatchQC/man/BatchQCout-class.Rd
Fixing some indentation and shortening lines greater than 80 characters
Revision: 117902
Author: jspidlen
Date: 2016-05-26T19:51:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/NAMESPACE
Modified  /trunk/madman/Rpacks/flowQB/R/helperFunctions.R
Added  /trunk/madman/Rpacks/flowQB/inst/unitTests/test_fitted_ellipse_gate.R
Modified  /trunk/madman/Rpacks/flowQB/man/fitted_ellipse_gate.Rd
More functionality back and more refactoring.
Revision: 117901
Author: v.obenchain
Date: 2016-05-26T19:18:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
update file name in collate field
Revision: 117900
Author: jspidlen
Date: 2016-05-26T19:04:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/NAMESPACE
Modified  /trunk/madman/Rpacks/flowQB/R/helperFunctions.R
Modified  /trunk/madman/Rpacks/flowQB/man/find_peak.Rd
Added  /trunk/madman/Rpacks/flowQB/man/fitted_ellipse_gate.Rd
Deleted  /trunk/madman/Rpacks/flowQB/man/scatter_gate.Rd.original
Adding functionality back and refactoring.
Revision: 117898
Author: p.hickey
Date: 2016-05-26T18:54:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicTuples/README.Rmd
Fix typo, tupels -> tuples

From: C. Titus Brown <titus@idyll.org>
Revision: 117897
Author: p.hickey
Date: 2016-05-26T18:54:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicTuples/README.Rmd
Typo

From: Peter Hickey <peter.hickey@gmail.com>
Revision: 117896
Author: p.hickey
Date: 2016-05-26T18:53:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicTuples/.Rbuildignore
Added  /trunk/madman/Rpacks/GenomicTuples/README.Rmd
Modified  /trunk/madman/Rpacks/GenomicTuples/README.md
Modified  /trunk/madman/Rpacks/GenomicTuples/paper.md
Response to JOSS review https://github.com/openjournals/joss-reviews/issues/20#issuecomment-219930496

From: Peter Hickey <peter.hickey@gmail.com>
Revision: 117895
Author: p.hickey
Date: 2016-05-26T18:53:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicTuples/paper.bib
Fixing bibtex entry.

From: Arfon Smith <arfon@users.noreply.github.com>
Revision: 117894
Author: p.hickey
Date: 2016-05-26T18:53:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicTuples/.Rbuildignore
Added  /trunk/madman/Rpacks/GenomicTuples/LICENSE
Modified  /trunk/madman/Rpacks/GenomicTuples/README.md
Added  /trunk/madman/Rpacks/GenomicTuples/paper.bib
Added  /trunk/madman/Rpacks/GenomicTuples/paper.json
Added  /trunk/madman/Rpacks/GenomicTuples/paper.md
Add JOSS submission

From: Peter Hickey <peter.hickey@gmail.com>
Revision: 117893
Author: d.tenenbaum
Date: 2016-05-26T18:46:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/deepSNV/DESCRIPTION
Modified  /trunk/madman/Rpacks/deepSNV/vignettes/shearwaterML.Rmd
Suggest rmarkdown, use rmarkdown::render instead of knitr::knitr
Revision: 117892
Author: v.obenchain
Date: 2016-05-26T18:29:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/grasp2db/vignettes/grasp2db.Rmd
missed one NHLBI_public
Revision: 117891
Author: v.obenchain
Date: 2016-05-26T18:28:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/grasp2db/DESCRIPTION
Modified  /trunk/madman/Rpacks/grasp2db/R/db_AnnotationHub.R
Modified  /trunk/madman/Rpacks/grasp2db/inst/scripts/grasp2AnnotationHub.R
Modified  /trunk/madman/Rpacks/grasp2db/vignettes/BiocGRASP2.Rmd
change hub path to NHLBI_public (small 'p' instead of capital 'P')
Revision: 117888
Author: h.corradabravo
Date: 2016-05-26T18:06:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Version bump
Revision: 117887
Author: h.corradabravo
Date: 2016-05-26T18:04:43+00:00
Paths:
Deleted  /trunk/madman/Rpacks/epivizr/inst/doc
Deleted  /trunk/madman/Rpacks/epivizr/inst/tests
Deleted  /trunk/madman/Rpacks/epivizr/inst/www
Deleted  /trunk/madman/Rpacks/epivizr/inst/www-full
delete empty directories after package restructure
Revision: 117886
Author: k.icay
Date: 2016-05-26T17:30:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/Director/DESCRIPTION
Modified  /trunk/madman/Rpacks/Director/R/functions.R
Modified  /trunk/madman/Rpacks/Director/inst/NEWS
Modified  /trunk/madman/Rpacks/Director/man/initSankey.Rd
Fixed example of initSankey function.
Revision: 117885
Author: l.shepherd
Date: 2016-05-26T16:02:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/R/VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/inst/unitTests/test_VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/man/VcfStack-class.Rd
Optimized Subsetting Methods

    -removed individual subsetting
    -added single subsetting method with "any" arguments

Revision: 117883
Author: l.shepherd
Date: 2016-05-26T13:19:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Added  /trunk/madman/Rpacks/GenomicFiles/inst/unitTests/test_VcfStack-class.R
Added Unit tests for VcfStack-class
Revision: 117882
Author: mtmorgan
Date: 2016-05-26T12:35:25+00:00
Paths:
Added  /trunk/madman/Rpacks/FunChIP
Added  /trunk/madman/Rpacks/FunChIP/DESCRIPTION
Added  /trunk/madman/Rpacks/FunChIP/NAMESPACE
Added  /trunk/madman/Rpacks/FunChIP/R
Added  /trunk/madman/Rpacks/FunChIP/R/choose.k.GRange.R
Added  /trunk/madman/Rpacks/FunChIP/R/cluster.GRange.R
Added  /trunk/madman/Rpacks/FunChIP/R/compute.d.GRange.R
Added  /trunk/madman/Rpacks/FunChIP/R/distance.GRange.R
Added  /trunk/madman/Rpacks/FunChIP/R/pileup.peak.GRange.R
Added  /trunk/madman/Rpacks/FunChIP/R/plot.GRange.R
Added  /trunk/madman/Rpacks/FunChIP/R/smooth.GRange.R
Added  /trunk/madman/Rpacks/FunChIP/R/summit.GRange.R
Added  /trunk/madman/Rpacks/FunChIP/data
Added  /trunk/madman/Rpacks/FunChIP/data/GR100.rda
Added  /trunk/madman/Rpacks/FunChIP/data/peaks.rda
Added  /trunk/madman/Rpacks/FunChIP/inst
Added  /trunk/madman/Rpacks/FunChIP/inst/NEWS
Added  /trunk/madman/Rpacks/FunChIP/inst/extdata
Added  /trunk/madman/Rpacks/FunChIP/inst/extdata/test.bam
Added  /trunk/madman/Rpacks/FunChIP/inst/extdata/test.bam.bai
Added  /trunk/madman/Rpacks/FunChIP/man
Added  /trunk/madman/Rpacks/FunChIP/man/FunChIP-package.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/GR100.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/choose_k-method.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/cluster_peak-method.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/compute_fragments_length.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/distance_peak.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/peaks.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/pileup_peak-method.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/plot_peak-method.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/smooth_peak-method.Rd
Added  /trunk/madman/Rpacks/FunChIP/man/summit_peak-method.Rd
Added  /trunk/madman/Rpacks/FunChIP/src
Added  /trunk/madman/Rpacks/FunChIP/src/Makevars
Added  /trunk/madman/Rpacks/FunChIP/src/Makevars.win
Added  /trunk/madman/Rpacks/FunChIP/src/kmean_function.cpp
Added  /trunk/madman/Rpacks/FunChIP/src/peak.h
Added  /trunk/madman/Rpacks/FunChIP/vignettes
Added  /trunk/madman/Rpacks/FunChIP/vignettes/FunChIP.Rnw
Added  /trunk/madman/Rpacks/FunChIP/vignettes/mybib.bib
Added  /trunk/madman/Rpacks/Pigengene
Added  /trunk/madman/Rpacks/Pigengene/DESCRIPTION
Added  /trunk/madman/Rpacks/Pigengene/NAMESPACE
Added  /trunk/madman/Rpacks/Pigengene/R
Added  /trunk/madman/Rpacks/Pigengene/R/add.noise.R
Added  /trunk/madman/Rpacks/Pigengene/R/balance.R
Added  /trunk/madman/Rpacks/Pigengene/R/bn.calculation.R
Added  /trunk/madman/Rpacks/Pigengene/R/bn.calculationS.R
Added  /trunk/madman/Rpacks/Pigengene/R/bn.module.R
Added  /trunk/madman/Rpacks/Pigengene/R/calculate.beta.R
Added  /trunk/madman/Rpacks/Pigengene/R/check.nas.R
Added  /trunk/madman/Rpacks/Pigengene/R/check.pigengene.input.R
Added  /trunk/madman/Rpacks/Pigengene/R/combinedPath.R
Added  /trunk/madman/Rpacks/Pigengene/R/combinedStrength.R
Added  /trunk/madman/Rpacks/Pigengene/R/compact.tree.R
Added  /trunk/madman/Rpacks/Pigengene/R/compute.pigengene.R
Added  /trunk/madman/Rpacks/Pigengene/R/consensus.R
Added  /trunk/madman/Rpacks/Pigengene/R/consensus.thresh.R
Added  /trunk/madman/Rpacks/Pigengene/R/dcor.matrix.R
Added  /trunk/madman/Rpacks/Pigengene/R/draw.bn.R
Added  /trunk/madman/Rpacks/Pigengene/R/draw.bnS.R
Added  /trunk/madman/Rpacks/Pigengene/R/draw.cor.R
Added  /trunk/madman/Rpacks/Pigengene/R/draw.cor.cond.R
Added  /trunk/madman/Rpacks/Pigengene/R/draw.improvement.R
Added  /trunk/madman/Rpacks/Pigengene/R/draw.module.sizes.R
Added  /trunk/madman/Rpacks/Pigengene/R/draw.scores.R
Added  /trunk/madman/Rpacks/Pigengene/R/dummyMaker.R
Added  /trunk/madman/Rpacks/Pigengene/R/enforce.blk.R
Added  /trunk/madman/Rpacks/Pigengene/R/gene.mapping.R
Added  /trunk/madman/Rpacks/Pigengene/R/get.combined.file.R
Added  /trunk/madman/Rpacks/Pigengene/R/get.consensus.files.R
Added  /trunk/madman/Rpacks/Pigengene/R/get.fitted.leaf.R
Added  /trunk/madman/Rpacks/Pigengene/R/get.genes.R
Added  /trunk/madman/Rpacks/Pigengene/R/get.module.data.file.R
Added  /trunk/madman/Rpacks/Pigengene/R/get.sorted.members.R
Added  /trunk/madman/Rpacks/Pigengene/R/get.used.features.R
Added  /trunk/madman/Rpacks/Pigengene/R/getALLRuns.R
Added  /trunk/madman/Rpacks/Pigengene/R/getBN.R
Added  /trunk/madman/Rpacks/Pigengene/R/hu.mouse.R
Added  /trunk/madman/Rpacks/Pigengene/R/indFileName.R
Added  /trunk/madman/Rpacks/Pigengene/R/learn.bn.R
Added  /trunk/madman/Rpacks/Pigengene/R/load.if.R
Added  /trunk/madman/Rpacks/Pigengene/R/make.bn.input.R
Added  /trunk/madman/Rpacks/Pigengene/R/make.decision.tree.R
Added  /trunk/madman/Rpacks/Pigengene/R/make.membership.queue.R
Added  /trunk/madman/Rpacks/Pigengene/R/message.if.R
Added  /trunk/madman/Rpacks/Pigengene/R/module.heatmap.R
Added  /trunk/madman/Rpacks/Pigengene/R/mtrim.R
Added  /trunk/madman/Rpacks/Pigengene/R/noise.analysis.R
Added  /trunk/madman/Rpacks/Pigengene/R/one.step.pigengene.R
Added  /trunk/madman/Rpacks/Pigengene/R/pheatmap.type.R
Added  /trunk/madman/Rpacks/Pigengene/R/plot.pigengene.R
Added  /trunk/madman/Rpacks/Pigengene/R/preds.at.R
Added  /trunk/madman/Rpacks/Pigengene/R/project.eigen.R
Added  /trunk/madman/Rpacks/Pigengene/R/pvalues.manova.R
Added  /trunk/madman/Rpacks/Pigengene/R/rename.nodes.R
Added  /trunk/madman/Rpacks/Pigengene/R/repeat.data.R
Added  /trunk/madman/Rpacks/Pigengene/R/sample.network.R
Added  /trunk/madman/Rpacks/Pigengene/R/save.if.R
Added  /trunk/madman/Rpacks/Pigengene/R/sbatch.R
Added  /trunk/madman/Rpacks/Pigengene/R/scoreCandidates.R
Added  /trunk/madman/Rpacks/Pigengene/R/unique.gene.names.R
Added  /trunk/madman/Rpacks/Pigengene/R/versrem.R
Added  /trunk/madman/Rpacks/Pigengene/R/welch.pvalue.R
Added  /trunk/madman/Rpacks/Pigengene/R/wgcna.one.step.R
Added  /trunk/madman/Rpacks/Pigengene/R/what.is.in.R
Added  /trunk/madman/Rpacks/Pigengene/R/which.cluster.R
Added  /trunk/madman/Rpacks/Pigengene/data
Added  /trunk/madman/Rpacks/Pigengene/data/aml.RData
Added  /trunk/madman/Rpacks/Pigengene/data/datalist
Added  /trunk/madman/Rpacks/Pigengene/data/eigengenes33.RData
Added  /trunk/madman/Rpacks/Pigengene/data/mds.RData
Added  /trunk/madman/Rpacks/Pigengene/data/pigengene.RData
Added  /trunk/madman/Rpacks/Pigengene/inst
Added  /trunk/madman/Rpacks/Pigengene/inst/CITATION
Added  /trunk/madman/Rpacks/Pigengene/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/Pigengene/man
Added  /trunk/madman/Rpacks/Pigengene/man/Pigengene-package.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/aml.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/balance.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/calculate.beta.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/check.pigengene.input.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/compact.tree.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/compute.pigengene.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/dcor.matrix.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/draw.bn.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/eigengenes33.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/gene.mapping.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/get.fitted.leaf.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/get.genes.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/get.used.features.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/learn.bn.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/make.decision.tree.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/mds.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/module.heatmap.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/one.step.pigengene.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/pheatmap.type.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/pigengene-class.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/pigengene.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/plot.pigengene.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/preds.at.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/project.eigen.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/pvalues.manova.Rd
Added  /trunk/madman/Rpacks/Pigengene/man/wgcna.one.step.Rd
Added  /trunk/madman/Rpacks/Pigengene/vignettes
Added  /trunk/madman/Rpacks/Pigengene/vignettes/Pigengene_inference.Rnw
Added  /trunk/madman/Rpacks/Pigengene/vignettes/pigengene.bib
Modified  /trunk/madman/Rpacks/bioc_3.4.manifest
Added  /trunk/madman/Rpacks/netprioR
Added  /trunk/madman/Rpacks/netprioR/DESCRIPTION
Added  /trunk/madman/Rpacks/netprioR/NAMESPACE
Added  /trunk/madman/Rpacks/netprioR/R
Added  /trunk/madman/Rpacks/netprioR/R/netprioR-class.R
Added  /trunk/madman/Rpacks/netprioR/R/netprioR-functions.R
Added  /trunk/madman/Rpacks/netprioR/R/netprioR-generics.R
Added  /trunk/madman/Rpacks/netprioR/R/netprioR-methods.R
Added  /trunk/madman/Rpacks/netprioR/R/netprioR-package.R
Added  /trunk/madman/Rpacks/netprioR/R/netprioR-simulation.R
Added  /trunk/madman/Rpacks/netprioR/README.md
Added  /trunk/madman/Rpacks/netprioR/data
Added  /trunk/madman/Rpacks/netprioR/data/simulation.rdata
Added  /trunk/madman/Rpacks/netprioR/inst
Added  /trunk/madman/Rpacks/netprioR/inst/NEWS
Added  /trunk/madman/Rpacks/netprioR/inst/example
Added  /trunk/madman/Rpacks/netprioR/inst/example/data_simulation.R
Added  /trunk/madman/Rpacks/netprioR/man
Added  /trunk/madman/Rpacks/netprioR/man/ROC-methods.Rd
Added  /trunk/madman/Rpacks/netprioR/man/bandwidth.Rd
Added  /trunk/madman/Rpacks/netprioR/man/cmn.Rd
Added  /trunk/madman/Rpacks/netprioR/man/conjugate_gradient.Rd
Added  /trunk/madman/Rpacks/netprioR/man/cuthill_mckee.Rd
Added  /trunk/madman/Rpacks/netprioR/man/fit-methods.Rd
Added  /trunk/madman/Rpacks/netprioR/man/laplacian.Rd
Added  /trunk/madman/Rpacks/netprioR/man/learn.Rd
Added  /trunk/madman/Rpacks/netprioR/man/netprioR-class.Rd
Added  /trunk/madman/Rpacks/netprioR/man/netprioR-package.Rd
Added  /trunk/madman/Rpacks/netprioR/man/norm_kern.Rd
Added  /trunk/madman/Rpacks/netprioR/man/plot.netprioR.Rd
Added  /trunk/madman/Rpacks/netprioR/man/ranks-methods.Rd
Added  /trunk/madman/Rpacks/netprioR/man/simulate_labels.Rd
Added  /trunk/madman/Rpacks/netprioR/man/simulate_network_random.Rd
Added  /trunk/madman/Rpacks/netprioR/man/simulate_network_scalefree.Rd
Added  /trunk/madman/Rpacks/netprioR/man/simulate_phenotype.Rd
Added  /trunk/madman/Rpacks/netprioR/man/simulation.Rd
Added  /trunk/madman/Rpacks/netprioR/man/weights-methods.Rd
Added  /trunk/madman/Rpacks/netprioR/vignettes
Added  /trunk/madman/Rpacks/netprioR/vignettes/netprioR.Rmd
Adding Pigengene, netprioR, FunChIP
Revision: 117880
Author: l.gatto
Date: 2016-05-26T10:11:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/MSnbase/NEWS
Modified  /trunk/madman/Rpacks/MSnbase/R/map.R
Modified  /trunk/madman/Rpacks/MSnbase/R/readMSData.R
Modified  /trunk/madman/Rpacks/MSnbase/R/utils.R
Modified  /trunk/madman/Rpacks/MSnbase/man/MzTab-class.Rd
Added  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_MSmap.R
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_MzTab.R
Added  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_MzTab_09.R
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-demo.Rnw
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-io.Rnw
Merge branch 'master' into devel

* master:
  fix map unit test
  remove useless getBins function
  don't export as.data.frame.MSmap - use as
  fix MSmap to dataframe coerce
  finish MSmap unit test
  update MSmap unittest
  update news
  MSmap unit testing and fix bug
  MSmap unit testing
  rearrange mzTab unit test - now counted in coverage
  update old googlecode url
  new gh dev version

From: Laurent <lg390@cam.ac.uk>
Revision: 117877
Author: s.manimaran
Date: 2016-05-26T06:41:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/BatchQC/DESCRIPTION
Modified  /trunk/madman/Rpacks/BatchQC/NAMESPACE
Modified  /trunk/madman/Rpacks/BatchQC/R/Circos.R
Modified  /trunk/madman/Rpacks/BatchQC/R/batchQC.R
Modified  /trunk/madman/Rpacks/BatchQC/R/batchtest.R
Modified  /trunk/madman/Rpacks/BatchQC/R/correlation.R
Modified  /trunk/madman/Rpacks/BatchQC/R/heatmap.R
Modified  /trunk/madman/Rpacks/BatchQC/R/pca.R
Modified  /trunk/madman/Rpacks/BatchQC/R/shapeAnalysis.R
Modified  /trunk/madman/Rpacks/BatchQC/R/simulate_data.R
Modified  /trunk/madman/Rpacks/BatchQC/R/sva.R
Modified  /trunk/madman/Rpacks/BatchQC/R/utils.R
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC_analyze.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC_condition_adjusted.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC_filter_genes.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC_fsva_adjusted.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC_num.sv.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC_shapeVariation.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC_sva.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchQC_svregress_adjusted.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchqc_circosplot.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchqc_correlation.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchqc_corscatter.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchqc_explained_variation.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchqc_heatmap.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchqc_pc_explained_variation.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchqc_pca.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchqc_pca_svd.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/batchtest.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/combatPlot.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/example_batchqc_data.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/getShinyInput.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/getShinyInputCombat.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/getShinyInputOrig.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/getShinyInputSVA.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/getShinyInputSVAf.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/getShinyInputSVAr.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/log2CPM.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/makeSVD.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/pcRes.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/plotPC.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/rnaseq_sim.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/setShinyInput.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/setShinyInputCombat.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/setShinyInputOrig.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/setShinyInputSVA.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/setShinyInputSVAf.Rd
Modified  /trunk/madman/Rpacks/BatchQC/man/setShinyInputSVAr.Rd
Updating all the examples with the updated rnaseq_sim function and fixing some BioCCheck warnings
Revision: 117876
Author: s.su
Date: 2016-05-26T05:05:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/Glimma/DESCRIPTION
Modified  /trunk/madman/Rpacks/Glimma/inst/NEWS
Bumped version
Revision: 117875
Author: jq.sun
Date: 2016-05-26T02:27:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCC/DESCRIPTION
update plot function.
Revision: 117874
Author: jq.sun
Date: 2016-05-26T02:27:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCC/R/TCC.plotMA.R
update plot function.
Revision: 117872
Author: jspidlen
Date: 2016-05-25T23:19:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/inst/NEWS
Added  /trunk/madman/Rpacks/flowQB/inst/unitTests
Added  /trunk/madman/Rpacks/flowQB/inst/unitTests/test_find_peak.R
Added  /trunk/madman/Rpacks/flowQB/tests
Added  /trunk/madman/Rpacks/flowQB/tests/runTests.R
Modified  /trunk/madman/Rpacks/flowQB/vignettes/flowQBVignettes.Rnw
Adding tests and resolving various check and BiocCheck issues.
Revision: 117871
Author: jspidlen
Date: 2016-05-25T22:58:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/NAMESPACE
Modified  /trunk/madman/Rpacks/flowQB/R/helperFunctions.R
Modified  /trunk/madman/Rpacks/flowQB/man/find_peak.Rd
Modified  /trunk/madman/Rpacks/flowQB/vignettes/flowQBVignettes.Rnw
Resolving various check and BiocCheck issues
Revision: 117870
Author: y.liao
Date: 2016-05-25T22:42:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/HelperFunctions.c
Modified  /trunk/madman/Rpacks/Rsubread/src/SNPCalling.c
Modified  /trunk/madman/Rpacks/Rsubread/src/core.c
Modified  /trunk/madman/Rpacks/Rsubread/src/input-files.c
Modified  /trunk/madman/Rpacks/Rsubread/src/input-files.h
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
(1) probing max file pointers in featureCounts ; (2) allJunctions overshot chromosome bug
Revision: 117869
Author: jspidlen
Date: 2016-05-25T22:37:37+00:00
Paths:
Deleted  /trunk/madman/Rpacks/flowQB/inst/doc
Cleaning up
Revision: 117868
Author: jspidlen
Date: 2016-05-25T22:19:17+00:00
Paths:
Deleted  /trunk/madman/Rpacks/flowQB/R/flowQBCOMPACTEDFUNCTIONS_R.R
Added  /trunk/madman/Rpacks/flowQB/R/flowQBCOMPACTEDFUNCTIONS_R.R.original
Refactoring.
Revision: 117867
Author: jspidlen
Date: 2016-05-25T22:18:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Refactoring.
Revision: 117866
Author: jspidlen
Date: 2016-05-25T22:14:21+00:00
Paths:
Deleted  /trunk/madman/Rpacks/flowQB/man/flowQB-package.Rd
Added  /trunk/madman/Rpacks/flowQB/man/flowQB-package.Rd.original
Refactoring.
Revision: 117864
Author: jspidlen
Date: 2016-05-25T21:45:22+00:00
Paths:
Added  /trunk/madman/Rpacks/flowQB/man/find_peak.Rd
Deleted  /trunk/madman/Rpacks/flowQB/man/find_peak.Rd.original
Putting find_peak back
Revision: 117863
Author: jspidlen
Date: 2016-05-25T21:34:06+00:00
Paths:
Added  /trunk/madman/Rpacks/flowQB/R/helperFunctions.R
Starting refactoring.
Revision: 117862
Author: jspidlen
Date: 2016-05-25T21:33:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/NAMESPACE
Modified  /trunk/madman/Rpacks/flowQB/R/flowQBCOMPACTEDFUNCTIONS_R.R
Starting refactoring.
Revision: 117860
Author: a.lun
Date: 2016-05-25T20:38:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/diffHic/inst/NEWS.Rd
Bumped version number in NEWS.
Revision: 117857
Author: m.jiang
Date: 2016-05-25T19:55:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/NAMESPACE
Modified  /trunk/madman/Rpacks/openCyto/R/gtMethod-methods.R
import parameters from flowCore to avoid warnings when openCyto is imported by others.
Revision: 117856
Author: p.haverty
Date: 2016-05-25T18:47:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Modified  /trunk/madman/Rpacks/genoset/NAMESPACE
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Modified  /trunk/madman/Rpacks/genoset/man/pos-methods.Rd
Version: 1.29.4. 'pos' generic is now imported from GenomicRanges
Revision: 117855
Author: p.haverty
Date: 2016-05-25T18:40:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Version: 1.29.3. subsetting uses rowRanges getter rather than direct access
Revision: 117854
Author: m.jiang
Date: 2016-05-25T18:35:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/NAMESPACE
Added  /trunk/madman/Rpacks/openCyto/R/toggle.helperGates.R
Added  /trunk/madman/Rpacks/openCyto/man/toggle.helperGates.Rd
add toggle.helperGates
Revision: 117851
Author: d.tenenbaum
Date: 2016-05-25T18:10:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/bamsignals/DESCRIPTION
Modified  /trunk/madman/Rpacks/csaw/DESCRIPTION
Modified  /trunk/madman/Rpacks/deepSNV/DESCRIPTION
Modified  /trunk/madman/Rpacks/diffHic/DESCRIPTION
Bump version of packages that directly depend on Rhtslib, now that it is
linking against htslib statically.
Revision: 117850
Author: d.tenenbaum
Date: 2016-05-25T18:06:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rhtslib/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rhtslib/R/zzz.R
Link htslib statically
Revision: 117849
Author: l.shepherd
Date: 2016-05-25T17:10:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/R/VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/man/VcfStack-class.Rd
Add Subsetting Functions and update readVcfStack

Revision: 117847
Author: p.blattmann
Date: 2016-05-25T15:43:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/SWATH2stats/NEWS
Modified  /trunk/madman/Rpacks/SWATH2stats/R/convert4MSstats.R
v1.3.4b update message in convert4MSstats.R

From: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Revision: 117845
Author: m.scherer
Date: 2016-05-25T15:20:56+00:00
Paths:
Added  /trunk/madman/Rpacks/RnBeads/man/add.age.histogram.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/add.agecomparison.plot.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/add.combination.plot.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/add.error.plot.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/add.quantile.plot.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/age.anti.transformation.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/age.transformation.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/agePredictor.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/agePredictor450.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/agePredictorRRBS.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/createPredictor.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/cv.array.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/cv.biseq.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/general.cv.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/imputeRRBS.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/rnb.execute.age.prediction.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/rnb.execute.training.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/rnb.section.ageprediction.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/rnb.step.ageprediction.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/run.cross.validation.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/simpleGlmnet.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/simpleGlmnetEvaluate.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/simpleGlmnetRRBS.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/trainPredictor.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/writePredictorToCsv.Rd
More documentation on age prediction
Revision: 117844
Author: m.scherer
Date: 2016-05-25T15:14:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/DESCRIPTION
Modified  /trunk/madman/Rpacks/RnBeads/NAMESPACE
Modified  /trunk/madman/Rpacks/RnBeads/R/agePrediction.R
Running devtools for documentation of the new functions in the age prediction
Revision: 117843
Author: p.blattmann
Date: 2016-05-25T14:45:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/SWATH2stats/DESCRIPTION
Modified  /trunk/madman/Rpacks/SWATH2stats/NEWS
Modified  /trunk/madman/Rpacks/SWATH2stats/R/convert4mapDIA.R
Modified  /trunk/madman/Rpacks/SWATH2stats/R/plot_correlation_between_samples.R
Modified  /trunk/madman/Rpacks/SWATH2stats/R/plot_variation.R
Modified  /trunk/madman/Rpacks/SWATH2stats/man/SWATH2stats-package.Rd
Modified  /trunk/madman/Rpacks/SWATH2stats/man/plot_correlation_between_samples.Rd
Modified  /trunk/madman/Rpacks/SWATH2stats/tests/testthat/test_convert.R
v1.3.4: convert4mapDIA: improve error message; plot_correlation_between_samples: add label option; plot_variation; DESCRIPTION

From: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Revision: 117839
Author: m.scherer
Date: 2016-05-25T13:20:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/R/main.R
Modified  /trunk/madman/Rpacks/RnBeads/inst/extdata/options.txt
Added options inference.age.prediction.cv and inference.age.column
Revision: 117838
Author: m.scherer
Date: 2016-05-25T13:19:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/vignettes/RnBeads.Rnw
Added age prediction section to package vignette
Revision: 117837
Author: m.scherer
Date: 2016-05-25T13:19:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/R/agePrediction.R
Added cross validation for training function
Revision: 117836
Author: l.shepherd
Date: 2016-05-25T13:00:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/R/VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/man/VcfStack-class.Rd
Updated Constructor

  - no arguments have to be specified
  - auto generates seqinfo if not provided
  - auto generates colData if not provided
  - removed VcfHeader information from object
  - removed automatic subsetting of seqinfo object

Revision: 117835
Author: mtmorgan
Date: 2016-05-25T13:00:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocInstaller/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocInstaller/R/updateBiocInstaller.R
bugfix: unload rather than detach BiocInstaller on update

- also, catch failed attempts to unload for more informative error message
Revision: 117833
Author: f.marini
Date: 2016-05-25T09:41:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/pcaExplorer/R/pcaExplorer.R
mini fix for color assignments in genespca

From: Federico Marini <marinif@uni-mainz.de>
Revision: 117832
Author: k.bemis
Date: 2016-05-25T08:23:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/Cardinal/NEWS
Modified  /trunk/madman/Rpacks/Cardinal/R/methods-SImageData.R
v1.4.1 fixed SImageData subset bug
Revision: 117830
Author: a.oles
Date: 2016-05-25T07:58:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBImage/R/Image.R
version 4.15.3
- `readImage`: use `vapply` instead of `abind` to reduce memory footprint

From: aoles <andrzej.oles@gmail.com>
Revision: 117829
Author: j.rainer
Date: 2016-05-25T07:16:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/DESCRIPTION
Modified  /trunk/madman/Rpacks/ensembldb/R/Methods.R
Modified  /trunk/madman/Rpacks/ensembldb/inst/NEWS
Modified  /trunk/madman/Rpacks/ensembldb/inst/unitTests/test_Functionality.R
Fix another bug in exonsBy.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 117828
Author: j.rainer
Date: 2016-05-25T06:38:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/DESCRIPTION
Modified  /trunk/madman/Rpacks/ensembldb/inst/NEWS
Merge finished.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 117827
Author: j.rainer
Date: 2016-05-25T06:38:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/R/EnsDbFromGTF.R
Modified  /trunk/madman/Rpacks/ensembldb/R/Methods.R
Modified  /trunk/madman/Rpacks/ensembldb/inst/NEWS
Bug fixes

o Column tx_id was always removed from exonsBy result even if in the
  columns argument.
o exon_idx was of type character if database generated from a GTF file.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 117826
Author: j.rainer
Date: 2016-05-25T06:38:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/inst/NEWS
Update NEWS and DESCRIPTION.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 117824
Author: s.manimaran
Date: 2016-05-25T04:53:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/BatchQC/R/simulate_data.R
Modified  /trunk/madman/Rpacks/BatchQC/inst/example/batchqc_pipeline.R
Modified  /trunk/madman/Rpacks/BatchQC/tests/testthat/test_batchQC.R
Modified  /trunk/madman/Rpacks/BatchQC/vignettes/BatchQCIntro.Rmd
Modified  /trunk/madman/Rpacks/BatchQC/vignettes/BatchQC_examples.Rmd
Modified  /trunk/madman/Rpacks/BatchQC/vignettes/BatchQC_usage_advanced.Rmd
Changing the parameter for the example simulated dataset to lower the batch and condition variation for SVA to work well
Revision: 117819
Author: m.riester
Date: 2016-05-24T23:04:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/runAbsoluteCN.R
Added message when intervals and SNVs not overlap.
Revision: 117818
Author: hpages
Date: 2016-05-24T22:37:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Deleted  /trunk/madman/Rpacks/IRanges/R/subsetting-internals.R
Added  /trunk/madman/Rpacks/IRanges/R/subsetting-utils.R
NSBS() generic (defined in S4Vectors) got new allow.NAs argument
Revision: 117817
Author: hpages
Date: 2016-05-24T22:34:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/R/DataFrame-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/Rle-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/subsetting-utils.R
normalizeSingleBracketSubscript() gets new 'allow.NAs' argument. This is used
in the "extractROWS" methods for atomic vectors and DataFrame objects to enable
support of NAs in the subscript.

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