R/gcFracOneRange.R

In ArrayTV: Implementation of wave correction for arrays

gcFracOneRange <- function(schr, starts, increm, maxwin, verbose = FALSE) {
    if (verbose) 
        message("Getting gc content From BS genome Object")
    Hsapiens <- get("Hsapiens")
    pregcFrac <- letterFrequencyInSlidingView(Hsapiens[[schr]], view.width = increm, 
        "CG", as.prob = T)
    if (verbose) 
        message("gc content stored")
    startinds <- rep(starts, each = maxwin/increm) + rep(seq(0, maxwin - increm, 
        increm), length(starts))
    startindbackwards <- rep(starts, each = maxwin/increm) - rep(seq(increm, maxwin, 
        increm), length(starts))
    
    
    startinds[which(startinds < 1)] <- 1
    startinds[which(startinds > length(pregcFrac))] <- length(pregcFrac)
    gcFrac1 <- pregcFrac[startinds]
    gcFrac1[is.na(gcFrac1)] <- 0
    
    startindbackwards[which(startindbackwards < 1)] <- 1
    startindbackwards[which(startindbackwards > length(pregcFrac))] <- length(pregcFrac)
    gcFracbackwards1 <- pregcFrac[startindbackwards]
    gcFracbackwards1[is.na(gcFracbackwards1)] <- 0
    
    return(round((gcFrac1 + gcFracbackwards1)/2, 3))
}