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merge collab branch

* collab:
update vignettes/Makefile
update .gitignore
update table in CopyNumberViewiew
bump dependency on oligoClasses version
Update alias for "[" method for PredictionRegion objects
Replaced CopyNumberOverview and Infrastructure vignettes with those in the release branch. The versions in release have removed AffymetrixPreprocessCN, which is no longer available

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71322 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2012 04:49:34
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 inst/scripts/SmoothingRawCN.pdf
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+AffyGW-snr.pdf
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+AffyGW.R
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+IlluminaPreprocessCN-snr.pdf
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+IlluminaPreprocessCN.bbl
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+IlluminaPreprocessCN.blg
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+gender.R
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+runAffy.R.sh
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+runIlluminaPreprocessCN.R.sh
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+preproc_debug.R
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+rowMediansByGenotype.c
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+SimpleUsage.R
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+copynumber.pdf
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+crlmmDownstream.Rnw
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fix typo in .gitignore

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58628 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:46:02
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 copynumber.R
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 runcopynumber.R
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-inst/scripts/SmoothingRawCn.pdf
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+inst/scripts/SmoothingRawCN.pdf
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 inst/scripts/test
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 .gitignore
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update .gitignore to ignore inst/scripts/SmoothingRawCN.pdf

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58627 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:45:57
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 copynumber.R
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+inst/scripts/SmoothingRawCn.pdf
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+inst/scripts/test
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+.gitignore
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gitignore ignores tmp.* debug.* and test.*

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58618 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:45:10
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 .auto*
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+CopyNumberOverview.pdf
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+test.*
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+debug.*
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 *.aux
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 *.dvi
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 cnvignette.org
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Add vignettes for copy number analysis. Add crlmmGT2.R file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@54171 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/03/2011 02:41:00
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+cnvignette.org
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 test/*
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 *.o
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 *.so
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Rewrote illumina_copynumber vignette. Add functions and docmentation for constructInf, preprocessInf, and genotypeInf.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@54164 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/03/2011 02:40:07
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change cnSet$SNR and cnSet$SKW to numeric (previously ff)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53657 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 12/03/2011 19:56:02
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-*.o
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 *.tex
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 illumina_copynumber-*
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 Makefile2
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update sample.CNSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53580 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2011 19:31:11
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add structure for unit tests (currently empty)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52982 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/02/2011 19:17:55
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 *.png
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 *~
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 relocating*
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+push
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+pull
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+copynumber.R
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+runcopynumber.R
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+runillumina.R
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commit after bioc rebase

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52859 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 16:19:11
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ignore ffobjs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52848 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:59:09
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fix for finding index of nonpolymorphic markers in genotype function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50887 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:21:45
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 illumina_copynumber-*
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 Makefile2
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genotype function should be independent of annotation package version

no longer uses ffrowapply. Updates assayData elements of callSet column by column

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50807 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/11/2010 04:13:23
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Update summarizeNps function for illumina platform

- A scatterplot of the A and B channels at nonpolymophic loci shows
that one channel appears to be background and the other channel
appears to be signal.

- A quick fix for CN estimation is to replace the normalized
intensities at nonpolymorphic loci for the A allele with the average
from both channels on the intensity scale ((A+B)/2)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50353 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/10/2010 13:43:06
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 copynumber-*
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Add illumina_copynumber.pdf to package.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49895 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2010 02:21:53
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.gitignore ignores copynumber-* and copynumber.log

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49138 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:59
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moved totalCopyNumber method to oligoClasses package.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49129 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:26
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Ignoring auto and Makefile

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49128 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:24
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Ignoring auto* and Makefile

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49127 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:22
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begin commening the 'normal' matrix as this is not used.

Parts of the 'normal' matrix appear to be used in fit.lm4 -- the
wrapper for nonpolymorphic markers on X. Testing here will be needed
once these lines are commented.

Should snpflags and normal be part of the CNSet object an instantiated
upon initialization? I think so. snpflags need only be the same
dimension as the parameters and can be included in the
LinerModelParameter class.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48953 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:49:25
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Fixed cross-references that were not linked to a topic in CNSet-methods and copynumberAccessors Rd files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48952 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:49:20
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Edited Makefile as in Peng's compendium

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48921 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:47:07
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