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Merge branch 'collab'

* collab:
remove getCluster() calls and replace with parStatus()
update man pages for crlmm and genotype.Illumina with respect to the setup for parallelization
add neededPkgs argument to ocLapply calls in crlmmGT2
bump dependency on oligoClasses
Update R/crlmm-illumina.R
contructInf, preprocessInf and genotypeInf no longer exported

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64211 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/03/2012 02:52:50
Showing8 changed files

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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: 1.13.11
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+Version: 1.13.12
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 Date: 2010-12-10
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 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, 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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@@ -10,7 +10,7 @@ License: Artistic-2.0
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 Depends: R (>= 2.13.0),
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          methods,
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          Biobase (>= 2.15.0),
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-         oligoClasses (>= 1.17.29)
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+         oligoClasses (>= 1.17.34)
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 Imports: affyio (>= 1.19.2),
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          ellipse,
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          genefilter (>= 1.33.0),
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@@ -75,4 +75,4 @@ export(crlmm,
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        genotype.Illumina,
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        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
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 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
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-export(ABpanel, constructInf, preprocessInf, genotypeInf, validCEL, celDates)
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+export(ABpanel, validCEL, celDates)
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@@ -1541,7 +1541,7 @@ shrinkSummary <- function(object,
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 	}
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 	if(is.lds){
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 		##index.list <- splitIndicesByLength(marker.index, ocProbesets())
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-		if(!is.null(getCluster()) & isPackageLoaded("snow")){
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+		if(parStatus()){
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 			index.list <- splitIndicesByNode(marker.index)
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 		} else index.list <- splitIndicesByLength(marker.index, ocProbesets())
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 		ocLapply(seq(along=index.list),
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@@ -1595,7 +1595,7 @@ genotypeSummary <- function(object,
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 	FUN <- get(myf)
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 	if(is.lds){
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 		##index.list <- splitIndicesByLength(marker.index, ocProbesets())
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-		if(!is.null(getCluster()) & isPackageLoaded("snow")){
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+		if(parStatus()){
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 			index.list <- splitIndicesByNode(marker.index)
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 		} else index.list <- splitIndicesByLength(marker.index, ocProbesets())
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 		ocLapply(seq(along=index.list),
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@@ -2116,7 +2116,7 @@ estimateCnParameters <- function(object,
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 	myfun <- lmFxn(type[[1]])
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 	FUN <- get(myfun)
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 	if(is.lds){
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-		if(!is.null(getCluster()) & isPackageLoaded("snow")){
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+		if(parStatus()){
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 			index.list <- splitIndicesByNode(marker.index)
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 		} else index.list <- splitIndicesByLength(marker.index, ocProbesets())
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 		ocLapply(seq(along=index.list),
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@@ -1267,7 +1267,7 @@ preprocessInf <- function(cnSet,
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 	sampleBatches <- splitIndicesByNode(seq(length=ncol(cnSet)))
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 	mixtureParams = initializeBigMatrix("crlmmMixt-", 4, narrays, "double")
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 	ocLapply(seq_along(sampleBatches),
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-		 processIDAT,
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+		 crlmm:::processIDAT,
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 		 sampleBatches=sampleBatches,
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 		 sampleSheet=sampleSheet,
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 		 arrayNames=arrayNames,
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@@ -99,7 +99,8 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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 				   mIndex=mIndex, params=params,
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 				   cIndexes=cIndexes, SMEDIAN=SMEDIAN,
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 				   theKnots=theKnots, DF=DF, probs=probs,
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-				   batchSize=ocProbesets())
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+				   batchSize=ocProbesets(),
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+				   neededPkgs="crlmm")
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 	newparams <- vector("list", 3)
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 	names(newparams) <- c("centers", "scales", "N")
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 	newparams[["centers"]] <- do.call("rbind", lapply(newparamsBatch, "[[", 1))
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@@ -227,7 +228,8 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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 		 A=A, B=B, mixtureParams=mixtureParams, fIndex=fIndex,
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 		 mIndex=mIndex, params=params, cIndexes=cIndexes,
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 		 SMEDIAN=SMEDIAN, theKnots=theKnots, DF=DF, probs=probs,
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-		 regionInfo=regionInfo, batchSize=ocProbesets())
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+		 regionInfo=regionInfo, batchSize=ocProbesets(),
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+		 neededPkgs="crlmm")
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 	##  END MOVE TO C#######
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 	## ##################
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 	##
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@@ -60,6 +60,7 @@ calls.
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 <<ldpath,results=hide>>=
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 library(ff)
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+options(ffcaching="ffeachflush")
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 outdir <- paste("/local_data/r00/crlmm/", getRversion(), "/illumina_vignette", sep="")
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 ldPath(outdir)
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 dir.create(outdir, recursive=TRUE, showWarnings=FALSE)
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@@ -102,7 +102,10 @@ library(crlmm)
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 ## genotype 50K SNPs at a time
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 ocProbesets(50000)
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 ## setup cluster - 8 cores on the machine
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-setCluster(8, "SOCK")
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+library(doSNOW)
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+cl <- makeCluster(8, "SOCK")
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+registerDoSNOW(cl)
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+##setCluster(8, "SOCK")
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 path <- system.file("celFiles", package="hapmapsnp6")
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 cels <- list.celfiles(path, full.names=TRUE)
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@@ -129,8 +129,10 @@ example below indicates.}
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 	## to enable paralellization, set to TRUE
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 	if(FALSE){
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 		library(snow)
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-		## 10 workers
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-		setCluster(10, "SOCK")
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+		library(doSNOW)
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+		## with 10 workers
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+		cl <- makeCluster(10, type="SOCK")
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+		registerDoSNOW(cl)
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 	}
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 	## path to idat files
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 	datadir <- "/thumper/ctsa/snpmicroarray/illumina/IDATS/370k"