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updated pdf of illumina_copynumber vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/crlmm@49659 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 28/09/2010 01:36:19
Showing5 changed files

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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: 1.6.5
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+Version: 1.6.6
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 Date: 2010-08-30
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 Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>
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 Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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-All: copynumber crlmmDownstream clean
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+All: copynumber crlmmDownstream illumina_copynumber clean
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 copynumber: copynumber.pdf
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 	cp -p ../scripts/copynumber.pdf .
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@@ -6,5 +6,8 @@ copynumber: copynumber.pdf
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 crlmmDownstream: crlmmDownstream.pdf
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 	cp -p ../scripts/crlmmDownstream.pdf .
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+illumina_copynumber: illumina_copynumber.pdf
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+	cp -p ../scripts/illumina_copynumber.pdf .
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+
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 clean:
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 	-$(RM) -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex
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Binary files a/inst/doc/illumina_copynumber.pdf and b/inst/doc/illumina_copynumber.pdf differ
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@@ -107,6 +107,9 @@ if(!exists("crlmmResult")){
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 		range(protocolData(crlmmResult)$ScanDate)
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 		save(crlmmResult, file=file.path(outdir, "crlmmResult.rda"))
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 		rm(RG); gc()
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+	} else{
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+		message("Loading previously saved file...")
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+		load(file.path(outdir, "crlmmResult.rda"))
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 	}
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 }
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 @
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 hist(cnSet$SNR, breaks=15)
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 @
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-\begin{figure}[tbh]
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+\begin{figure}[t!]
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 <<firstSample, fig=TRUE>>=
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 low.snr <- which(cnSet$SNR == min(cnSet$SNR))
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 high.snr <- which(cnSet$SNR == max(cnSet$SNR))
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@@ -300,7 +303,7 @@ cn <- cn[!is.na(cn)]
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 y <- as.numeric(runmed(cn, k=3))
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 @
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-\section{Session information}
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+\section*{Session information}
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 <<sessionInfo, results=tex>>=
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 toLatex(sessionInfo())
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