Browse code

Add temporary code for checking MIN.SAMPLE in copynumber vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52843 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:58:50
Showing1 changed files

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@@ -54,8 +54,6 @@ separately) that are listed below.
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 pkgs <- annotationPackages()
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 pkgs <- pkgs[grep("Crlmm", pkgs)]
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 pkgs
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-library(snow)
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-setCluster(4, "SOCK")
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 @
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 Note that 'pd.genomewidesnp6' and 'genomewidesnp6Crlmm' are both
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@@ -74,7 +72,7 @@ if(getRversion() < "2.13.0"){
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 	rpath <- getRversion()
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 } else rpath <- "trunk"
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 ##outdir <- paste("/thumper/ctsa/snpmicroarray/rs/ProcessedData/crlmm/", rpath, "/copynumber_vignette", sep="")
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-outdir <- "~/tmp"
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+outdir <- "/home/bst/student/rscharpf/tmp"
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 dir.create(outdir, recursive=TRUE, showWarnings=FALSE)
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 @
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@@ -108,9 +106,12 @@ we extract the population identifier from the CEL file names and
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 assign these identifiers to the variable \Robject{batch}.
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 <<celfiles>>=
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-celFiles <- list.celfiles(pathToCels, full.names=TRUE, pattern=".CEL")[1:10]
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+celFiles <- list.celfiles(pathToCels, full.names=TRUE, pattern=".CEL")
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 celFiles <- celFiles[substr(basename(celFiles), 13, 13) %in% c("C", "Y")]
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 batch <- as.factor(substr(basename(celFiles), 13, 13))
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+sample.index <- c(sample(which(batch == "C"), 15), sample(which(batch == "Y"), 11))
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+celFiles <- celFiles[sample.index]
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+batch <- batch[sample.index]
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 @
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 The preprocessing steps for copy number estimation includes quantile
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@@ -191,7 +192,11 @@ The \Rfunction{crlmmCopynumber} performs the following steps:
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   displayed during the processing.
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 <<LDS_copynumber>>=
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-cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet)
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+GT.CONF.THR <- 0.8
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+cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR,
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+		     MIN.SAMPLES=12)
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+cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR,
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+		     MIN.SAMPLES=11)
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 @
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 In an effort to reduce I/O, the \Rpackage{crlmmCopynumber} function no
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@@ -618,6 +623,11 @@ detection and removal may be explored in the future.
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 Copy number estimates for other chromosomes, such as mitochondrial and
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 chromosome Y, are not currently available in \crlmm{}.
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+
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+\section{Different batch structure.}
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+
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 <<echo=FALSE>>=
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 invisible(close(cnSet))
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 @