Browse code

Use bb <- getOption("ffbatchbytes") throughout crlmm-illumina

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52839 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:58:36
Showing1 changed files

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@@ -120,7 +120,7 @@ readIdatFiles = function(sampleSheet=NULL,
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 	       }
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 	       rm(G)
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 	       gc()
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-	       if(verbose) { 
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+	       if(verbose) {
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                       cat(paste(sep, fileExt$red, sep=""), "\n")
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 	       }
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 	       R = readIDAT(redidats[i])
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@@ -589,7 +589,7 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5,
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     # separate out copy number probes
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   npIndex = getVarInEnv("npProbesFid")
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   nprobes = length(npIndex)
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-  
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+
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   if(length(nprobes)>0) {
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      A = matrix(as.integer(exprs(channel(XY, "X"))[npIndex,]), nprobes, narrays)
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      B = matrix(as.integer(exprs(channel(XY, "Y"))[npIndex,]), nprobes, narrays)
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@@ -1126,7 +1126,7 @@ genotype.Illumina = function(sampleSheet=NULL,
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 	callSet <- construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,
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 				      ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,
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 				      highDensity=highDensity, sep=sep, fileExt=fileExt,
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-				      cdfName=cdfName, copynumber=copynumber, verbose=verbose, batch=batch, # fns=fns, 
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+				      cdfName=cdfName, copynumber=copynumber, verbose=verbose, batch=batch, # fns=fns,
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 				      saveDate=saveDate) #, outdir=outdir)
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 	if(missing(sns)) sns = sampleNames(callSet)
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     if(is.lds) {
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@@ -1149,7 +1149,7 @@ genotype.Illumina = function(sampleSheet=NULL,
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                  sep=sep, fileExt=fileExt, saveDate=saveDate, verbose=verbose, mixtureSampleSize=mixtureSampleSize,
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                  fitMixture=fitMixture, eps=eps, seed=seed, cdfName=cdfName, sns=sns, stripNorm=stripNorm,
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                  useTarget=useTarget, A=A(callSet), B=B(callSet), SKW=SKW, SNR=SNR,
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-                 mixtureParams=mixtureParams, is.snp=is.snp, neededPkgs=c("crlmm", pkgname)) # outdir=outdir, 
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+                 mixtureParams=mixtureParams, is.snp=is.snp, neededPkgs=c("crlmm", pkgname)) # outdir=outdir,
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           open(SKW)
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           open(SNR)
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@@ -1196,8 +1196,8 @@ genotype.Illumina = function(sampleSheet=NULL,
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           open(A(callSet))
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           open(B(callSet))
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           tmpA = initializeBigMatrix(name="A", length(snp.index), narrays)
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-          tmpB = initializeBigMatrix(name="B", length(snp.index), narrays) 
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-#          bb = getOption("ffbatchbytes")          
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+          tmpB = initializeBigMatrix(name="B", length(snp.index), narrays)
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+#          bb = getOption("ffbatchbytes")
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 #          bb = ocProbesets()*length(sns)*8
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 		  ffcolapply(tmpA[,i1:i2] <- A(callSet)[snp.index,i1:i2], X=A(callSet)) #, BATCHBYTES=bb) # X=A(callSet)[snp.index,]
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 		  ffcolapply(tmpB[,i1:i2] <- B(callSet)[snp.index,i1:i2], X=B(callSet)) #, BATCHBYTES=bb) # X=B(callSet)[snp.index,]
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@@ -1293,7 +1293,7 @@ processIDAT =  function(sel, sampleSheet=NULL,
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         gc()
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 	    if(verbose) message("Finished preprocessing.")
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         snp.index = which(is.snp)
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-	    np.index = which(!is.snp)
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+	np.index = which(!is.snp)
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 #        open(res[["A"]])
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 #        open(res[["B"]])
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@@ -1309,7 +1309,7 @@ processIDAT =  function(sel, sampleSheet=NULL,
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 	    if(length(np.index)>0) {
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 #			for (j in 1:length(sel)) {
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 			ffcolapply(A[np.index,sel][,i1:i2] <- res[["cnAB"]]$A[,i1:i2], X=res[["cnAB"]]$A)
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-			ffcolapply(B[np.index,sel][,i1:i2] <- res[["cnAB"]]$B[,i1:i2], X=res[["cnAB"]]$B)		  
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+			ffcolapply(B[np.index,sel][,i1:i2] <- res[["cnAB"]]$B[,i1:i2], X=res[["cnAB"]]$B)
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 #            A[np.index, sel[j]] = res[["cnAB"]]$A[,j]
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 #            B[np.index, sel[j]] = res[["cnAB"]]$B[,j]
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 #          }