git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59151 bc3139a8-67e5-0310-9ffc-ced21a209358
unknown authored on 13/10/2011 05:28:47
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@@ -443,6 +443,91 @@ readBPM <- function(bpmFile){
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} |
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+readGenCallOutput = function(file, path=".", cdfName, verbose=FALSE) {
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+ if(verbose) |
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+ cat("Reading", file, "\n")
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+ tmp=readLines(file.path(path,file),n=15) |
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+ s=c("\t",",")
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+ a=unlist(strsplit(tmp[10][1],s[1])) |
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+ if(length(a)!=1){
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+ sepp=s[1] |
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+ a1=unlist(strsplit(tmp[10][1],s[1])) |
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+ } |
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+ if(length(a)==1){
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+ sepp=s[2] |
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+ a1=unlist(strsplit(tmp[10][1],s[2])) |
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+ } |
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+ |
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+ b=c("Sample ID","SNP Name","Allele1 - Forward","Allele2 - Forward","GC Score","X Raw","Y Raw")
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+ b2=c("GC Score","X Raw","Y Raw")
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+ |
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+ m1=m=match(a1,b) |
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+ m2=match(a1,b2) |
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+ m[is.na(m)==FALSE]<-list(character(0)) |
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+ m[is.na(m2)==FALSE]<-list(numeric(0)) |
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+ m[is.na(m)==TRUE]<-list(NULL) |
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+ names(m)<-paste(b[m1],names(m),sep='') |
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+ |
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+ fc = file(file.path(path, file), open="r") |
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+ |
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+ dat = scan(fc, what=m, skip=10,sep=sepp) |
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+ close(fc) |
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+ |
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+ samples = unique(dat$"Sample ID") |
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+ nsamples = length(samples) |
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+ snps = unique(dat$"SNP Name") |
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+ nsnps = length(snps) |
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+ if(verbose) |
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+ cat("Check ordering for samples","\n")
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+ |
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+ X = Y = zeroes = matrix(0, nsnps, nsamples) |
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+ |
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+ for(i in 1:length(samples)) {
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+ ind = dat$"Sample ID"==samples[i] |
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+ if(sum(dat$"SNP Name"[ind]==snps)==nsnps) {
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+ if(verbose) |
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+ cat(paste("Correct ordering for sample", samples[i], "\n"))
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+ X[,i] = dat$"X Raw"[ind] |
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+ Y[,i] = dat$"Y Raw"[ind] |
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+ gc() |
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+ } |
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+ if(sum(dat$"SNP Name"[ind]==snps)!=nsnps) {
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+ if(verbose) |
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+ cat("Reordering sample ", samples[i],"\n")
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+ m=match(snps,dat$"SNP Name"[ind]) |
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+ X[,i]= dat$"X Raw"[ind][m] |
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+ Y[,i]= dat$"Y Raw"[ind][m] |
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+ } |
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+ } |
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+ |
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+# samplenamescorrect = gsub("(_R.)|(_R$)", "", samples)
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+ zeroes=(X=="0"|Y=="0") |
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+ colnames(X) = colnames(Y) = colnames(zeroes) = samples #namescorrect |
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+ rownames(X) = rownames(Y) = snps |
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+ |
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+ if(verbose) |
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+ cat("Creating NChannelSet object\n")
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+ |
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+# if (getRversion() < "2.13.0") {
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+# rpath <- getRversion() |
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+# outdir <- paste(path, "/illumina_vignette", sep = "") |
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+# ldPath(outdir) |
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+# dir.create(outdir, recursive = TRUE, showWarnings = FALSE) |
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+# } |
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+ |
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+ XY = new("NChannelSet", X = initializeBigMatrix(name = "X", nr = nrow(X), nc = ncol(X), vmode = "integer", initdata=X),
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+ Y = initializeBigMatrix(name = "Y", nr = nrow(X), nc = ncol(X), vmode = "integer", initdata=Y), |
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+ zero = initializeBigMatrix(name = "zero", nr = nrow(X), nc = ncol(X), vmode = "integer", initdata=zeroes), |
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+ annotation = cdfName, storage.mode = "environment") |
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+ sampleNames(XY)=colnames(X) |
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+ |
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+ if(verbose) |
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+ cat("Done\n")
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+ |
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+ XY |
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+} |
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+ |
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+ |
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RGtoXY = function(RG, chipType, verbose=TRUE) {
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needToLoad <- !all(sapply(c('addressA', 'addressB', 'base'), isLoaded))
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