R/gcFracAllWin.R

In ArrayTV: Implementation of wave correction for arrays

gcFracAllWin <- function(maxwins, increms, chr, allstarts, samplechr, uniqchrs, strategyuse, 
    annotation.pkg, verbose = FALSE) {
    incremuse <- NULL
    gcFracBoth <- foreach(schr = uniqchrs[uniqchrs %in% samplechr], .combine = rbind, 
        .export = "gcFracOneRange", .packages = c(annotation.pkg, "ArrayTV")) %:% 
        foreach(incremuse = increms, .combine = cbind) %dopar% {
        starts <- allstarts[chr %in% schr]
        ## STRATEGY 1: This is not implemented if(strategyuse==1){ if(verbose)
        ## print(paste('vv is',vv) ) if(vv==1){ ranges <-
        ## IRanges(start=rep(starts,each=maxwin/increm/2)+rep(seq(0,(maxwin/2)-increm,increm),length(starts)),
        ## width=increm) }else if(vv==2){ ranges <-
        ## IRanges(start=rep(starts,each=maxwin/increm/2)+rep(seq((maxwin/2),maxwin-increm,increm),length(starts)),
        ## width=increm) }else if(vv==3){ ranges <-
        ## IRanges(start=rep(starts,each=maxwin/increm/2)-rep(seq(increm,maxwin/2,increm),length(starts)),
        ## width=increm) }else if(vv==4){ ranges <-
        ## IRanges(start=rep(starts,each=maxwin/increm/2)-rep(seq((maxwin/2)+increm,maxwin,increm),length(starts)),
        ## width=increm) } ranges[which(start(ranges) < 1)] <- IRanges(start=1,end=increm)
        ## if(verbose) print('before All views') inDNAset <- DNAStringSet() preinDNAset2
        ## <- DNAStringSet(Views(Hsapiens[[schr]],ranges))
        ## preinDNAset2[which(width(preinDNAset2) < increm)] <-
        ## DNAStringSet((paste(rep('N',increm),collapse=''))) inDNAset <-
        ## unlist(preinDNAset2)
        
        ## dnasetLen <- length(inDNAset) gcFrac <-
        ## letterFrequencyInSlidingView(inDNAset,view.width=increm,'CG',as.prob=T)[seq(1,dnasetLen,increm)]
        ## } END Strategy 1
        
        ## STRATEGY 2
        if (strategyuse == 2) 
            {
                schr <- gsub("23", "X", schr)
                schr <- gsub("24", "X", schr)
                
                
                maxwinuse <- maxwins[which(increms == incremuse)]
                gcFrac <- as.matrix(gcFracOneRange(schr, starts, incremuse, maxwinuse, 
                  verbose))
            }  ## end strategy 2
        gcFrac
    }  ## end foreach statement
    return(gcFracBoth)
}