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Fix table in CopyNumberOverview.Rnw

* collab_release:
update .gitignore
update .gitignore
update table in CopyNumberOverview vignette
Fix bug in calculateRBaf that can cause sample indices and batch indices to be misaligned when batch is not in alphabetical order
Update CopyNumberOverview and Infratructure vignettes

ignettes

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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/crlmm@71321 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2012 04:33:45
Showing4 changed files

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@@ -35,3 +35,16 @@ runillumina.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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+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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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.16.6
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+Version: 1.16.8
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
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@@ -548,7 +548,7 @@ calculateRBafCNSet <- function(object, batch.name, chrom){
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 	indexlist <- split(index, chr[index])
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 	J <- which(batch(object) %in% batch.name)
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 	sns <- sampleNames(object)[J]
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-	sampleindex <- split(J, batch(object)[J])
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+	sampleindex <- split(J, factor(batch(object)[J], levels=unique(batch(object)[J])))
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 	if(!all(valid.chrs)) warning("Only computing log R ratios and BAFs for autosomes and chr X")
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 	## if ff package is loaded, these will be ff objects
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 	chr <- names(indexlist)
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@@ -42,11 +42,10 @@ appropriate.
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 \begin{center}
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 \begin{tabular}{|lp{1.2in}p{1.5in}p{2in}|}
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 \hline
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- Vignette                &  Platform            &  Annotation package                        &  Scope                                               \\
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-\hline
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-Infrastructure          & Affy/Illumina                    & &  The CNSet container / large data support using the \Rpackage{ff} package            \\
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+ Vignette &  Platform &  Annotation package &  Scope \\ \hline
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+Infrastructure & Affy/Illumina & & The CNSet container / large data support using the \Rpackage{ff} package            \\
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  AffyGW  &  Affy 5.0, 6.0       &  genomewidesnp5Crlmm, genomewidesnp6Crlmm  &  Preprocessing, genotyping, CN estimation\\
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- IlluminaPreprocessCN    &  Illumina  &  several$^\dagger$ &  Preprocessing, genotyping, CN estimation
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+ IlluminaPreprocessCN    &  Illumina  &  several$^\dagger$ &  Preprocessing, genotyping, CN estimation\\
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 \hline
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 \end{tabular}
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 \end{center}