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Commented all of the cA, cB and CA(object) <- CB(object)<- assignments in lm.fit1 function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48930 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:47:48
Showing 3 changed files

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@@ -957,25 +957,20 @@ fit.lm1 <- function(idxBatch,
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 			phiA[phiA[, J] < MIN.PHI, J] <- MIN.PHI
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 			phiB[phiB[, J] < MIN.PHI, J] <- MIN.PHI
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 		}
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-		## formerly polymorphic():  calculate copy number
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-		cA[, k] <- matrix((1/phiA[, J]*(A-nuA[, J])), nrow(A), ncol(A))
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-		cB[, k] <- matrix((1/phiB[, J]*(B-nuB[, J])), nrow(B), ncol(B))
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+##		cA[, k] <- matrix((1/phiA[, J]*(A-nuA[, J])), nrow(A), ncol(A))
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+##		cB[, k] <- matrix((1/phiB[, J]*(B-nuB[, J])), nrow(B), ncol(B))
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 		rm(G, A, B, NORM, wA, wB, YA,YB, res, negA, negB, Np, Ns)
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 		gc()
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 	}
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-	cA[cA < 0.05] <- 0.05
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-	cB[cB < 0.05] <- 0.05
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-	cA[cA > 5] <-  5
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-	cB[cB > 5] <- 5
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-	cA <- matrix(as.integer(cA*100), nrow(cA), ncol(cA))
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-	cB <- matrix(as.integer(cB*100), nrow(cB), ncol(cB))
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+##	cA[cA < 0.05] <- 0.05
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+##	cB[cB < 0.05] <- 0.05
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+##	cA[cA > 5] <-  5
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+##	cB[cB > 5] <- 5
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+##	cA <- matrix(as.integer(cA*100), nrow(cA), ncol(cA))
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+##	cB <- matrix(as.integer(cB*100), nrow(cB), ncol(cB))
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+##	CA(object)[snps, ] <- cA
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+##	CB(object)[snps, ] <- cB
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-
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-	
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-	CA(object)[snps, ] <- cA
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-	CB(object)[snps, ] <- cB
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-
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-	
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 	snpflags[snps, ] <- flags
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 	lapply(lM(object), open)
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@@ -2,7 +2,6 @@
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 all:	illumina_copynumber copynumber 
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 copynumber:	copynumber.Rnw
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-##	echo "Sweave(\"$1.Rnw\"); library(tools); texi2dvi(\"$1.tex\", pdf=TRUE)" | R --no-save --no-restore;
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 	echo "Stangle(\"copynumber.Rnw\")" | R --no-save --no-restore;	
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 	cat ~/bin/cluster.template | perl -pe "s/Rprog/copynumber.R/" > copynumber.R.sh
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 	qsub -m e -r y -cwd -l mem_free=12G,h_vmem=16G copynumber.R.sh
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@@ -129,6 +129,7 @@ if(!file.exists(file.path(outdir, "cnSet.rda"))){
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 					   batch=batch[1:20])
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 	class(calls(gtSet.assayData_matrix))
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 }
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+q("no")
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 @ 
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 Next, we estimate copy number for the 20 CEL files.  The copy number
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@@ -140,11 +141,6 @@ will load \Robject{cnSet.assayData_matrix} from disk if this
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 computation had already been performed as part of the batch job.
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 <<copynumber>>=
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-stop()
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-tms1 <- system.time(tmp <- crlmmCopynumber(gtSet.assayData_matrix))
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-reload_pkg("crlmm")
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-trace(nuphiAllele, browser)
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-tms2 <- system.time(tmp <- crlmmCopynumber(gtSet.assayData_matrix))
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 cnSet.assayData_matrix <- checkExists("cnSet.assayData_matrix",
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 				      .path=outdir,
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 				      .FUN=crlmmCopynumber,