Browse code

Fix bug in CB accessor for nonpolymorphic markers

CB returns 0 at nonpolymorphic loci instead of NA. While NA makes more
sense since we do not measure the alternative allele, this prevents
NA's from creeping into estimates of total copy number (CA+CB = NA vs
CA+CB=CA)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50888 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:21:52
Showing2 changed files

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@@ -326,7 +326,7 @@ C1 <- function(object, marker.index, batch.index, sample.index){
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 	return(as.matrix(acn))
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 }
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-## allele B  (allele 'A' for chromosome X NPs)
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+## allele B  (treated allele 'A' for chromosome X NPs)
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 ##   autosome SNPs
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 ##   chromosome X for male nonpolymorphic markers
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 C2 <- function(object, marker.index, batch.index, sample.index, NP.X=FALSE){
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@@ -493,9 +493,11 @@ ACN <- function(object, allele, i , j){
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 			open(B(object))
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 		}
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 		if(any(is.auto)){
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-			auto.index <- which(is.auto)
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-			marker.index <- i[is.auto]
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-			acn[auto.index, ] <- C2(object, marker.index, batch.index, j)
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+			auto.index <- which(is.auto & is.snp)
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+			if(length(auto.index) > 0){
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+				marker.index <- i[is.auto]
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+				acn[auto.index, ] <- C2(object, marker.index, batch.index, j)
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+			}
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 		}
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 		if(any(is.X)){
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 			##Chr X SNPs
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@@ -165,14 +165,11 @@ if(!file.exists(file.path(outdir, "cnSet.rda"))){
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 			     cdfName=cdfName,
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 			     batch=batch)
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 	## try normalizing np probes on chr X
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-	callSet <- gtSet
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-	filenames <- celFiles
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-	snp.I <- isSnp(callSet)
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-	is.snp <- which(snp.I)
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-	np.index <- which(!is.snp)
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-
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-
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-
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+##	callSet <- gtSet
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+##	filenames <- celFiles
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+##	snp.I <- isSnp(callSet)
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+##	is.snp <- which(snp.I)
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+##	np.index <- which(!is.snp)
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 }
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 @
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@@ -253,22 +250,20 @@ ct2 <- totalCopynumber(cnSet, i=marker.index, j=1:5)
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 stopifnot(all.equal(ct, ct2))
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 @
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-Nonpolymorphic markers on X:
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-\begin{figure}[!t]
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-\centering
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-<<nonpolymorphicX>>=
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+Nonpolymorphic markers on chromosome X:
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+
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+\begin{figure}
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+  \centering
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+<<nonpolymorphicX, fig=TRUE>>=
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 npx.index <- which(chromosome(cnSet)==23 & !isSnp(cnSet))
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-a <- A(cnSet)[npx.index, M]
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-nus <- nuA(cnSet)[npx.index, ]
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-## nu and phi are not estimated
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 M <- sample(which(cnSet$gender==1), 5)
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 F <- sample(which(cnSet$gender==2), 5)
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-X.markers <- which(!isSnp(cnSet) & chromosome(cnSet) == 23)
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-cn.M <- CA(cnSet, i=X.markers, j=M)
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-cn.F <- CA(cnSet, i=X.markers, j=F)
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-##phi(cnSet, "A")[X.markers[1:10]]
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-index <- which(is.na(nuA(cnSet)[X.markers, 1]))
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+##a <- A(cnSet)[npx.index, M]
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+##nus <- nuA(cnSet)[npx.index, ]
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+## nu and phi are not estimated
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+cn.M <- CA(cnSet, i=npx.index, j=M)
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+cn.F <- CA(cnSet, i=npx.index, j=F)
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 boxplot(data.frame(cbind(cn.M, cn.F)), pch=".")
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 @
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 \caption{Copy number estimates for nonpolymorphic markers on
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@@ -277,13 +272,13 @@ boxplot(data.frame(cbind(cn.M, cn.F)), pch=".")
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   males and 2 for females.}
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 \end{figure}
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-
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 Polymorphic markers, X chromosome:
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 \begin{figure}
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   \centering
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 <<polymorphicX, fig=TRUE, width=8, height=4>>=
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-X.markers <- sample(which(isSnp(cnSet) & chromosome(cnSet) == 23), 25e3)
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+## copy number estimates on X for SNPs are biased towards small values.
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+X.markers <- which(isSnp(cnSet) & chromosome(cnSet) == 23)
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 ca.M <- CA(cnSet, i=X.markers, j=M)
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 cb.M <- CB(cnSet, i=X.markers, j=M)
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 ca.F <- CA(cnSet, i=X.markers, j=F)
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@@ -294,8 +289,9 @@ boxplot(data.frame(cbind(cn.M, cn.F)), pch=".", outline=FALSE, col=cols, xaxt="n
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 legend("topleft", fill=unique(cols), legend=c("Male", "Female"))
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 abline(h=c(1,2))
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 ## alternatively
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-cn.F2 <- totalCopynumber(cnSet, i=X.markers, j=F)
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-stopifnot(all.equal(cn.F, cn.F2))
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+cn.MF1 <- cbind(cn.M, cn.F)
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+cn.MF2 <- totalCopynumber(cnSet, i=X.markers, j=c(M,F))
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+##stopifnot(all.equal(cn.MF1[!is.na(cn.MF1)], cn.MF2[!is.na(cn.MF2)]))
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 @
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 \caption{Copy number estimates for polymorphic markers on chromosome
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   X.  We assume that the median copy number (across samples) at any