R/getGCinBestWindowGenome.R

In ArrayTV: Implementation of wave correction for arrays

getGCinBestWindowGenome <- function(gcFracBoth, starts, nparts, chr, samplechr, remainingChr, 
    increms, gmaxvals, gmaxvalsInd, tvScore, verbose = FALSE) {
    i <- NULL
    priorFracWremaining <- foreach(i = which(!duplicated(gmaxvalsInd)), .combine = "list", 
        .multicombine = TRUE, .export = "priorFracs", .packages = "ArrayTV") %dopar% 
        {
            if (verbose) 
                message(paste("A maximum first pass  TV is", gmaxvals[i], "in window", 
                  rownames(tvScore)[gmaxvalsInd[i]]))
            
            ## maximum tv score window
            maxuse1 <- gmaxvalsInd[i]
            
            priorFrac <- priorFracs(gcFracBoth, maxuse1, nparts, tvScore, increms)
            
            if (length(remainingChr) == 0) {
                priorFracWremaining <- priorFrac
            } else {
                ## Get GC for locations from non-sampled regions of genome
                forwardExtend <- as.numeric(rownames(tvScore)[maxuse1])
                reverseExtend <- forwardExtend
                
                priorFracWremaining <- priorFracsRestOfGenome(forwardExtend, reverseExtend, 
                  remainingChr, starts, chr)
                if (verbose) 
                  message(paste("forward extend", forwardExtend, "reverse extend", 
                    reverseExtend))
                
                priorFracWremaining[chr %in% samplechr] <- priorFrac
            }
            
            priorFracWremaining
        }
    return(priorFracWremaining)
}