R/makeWindowLookup.R

In Repitools: Epigenomic tools

makeWindowLookupTable <- function(indexes = NULL, offsets = NULL, starts = NULL, ends = NULL)
{
    if(is.null(indexes))
        stop("probe indexes not given.")
    if(is.null(offsets))
        stop("probe offsets not given.")
    if(is.null(starts))
        stop("starts of windows not given.")
    if(is.null(ends))
        stop("ends of windows not given.")

    lookupTable <- matrix(NA,nrow=length(indexes),ncol=length(starts))
    colnames(lookupTable) <- (starts+ends)/2
    rownames(lookupTable) <- names(indexes)

    ind <- unlist(indexes)
    off <- unlist(offsets, use.names=FALSE)
    genes <- unlist(mapply(rep, 1:length(indexes), sapply(indexes, length)))

    off.IRanges <- IRanges(start=off, width=1)
    o <- as.matrix(findOverlaps(query=off.IRanges, subject=IRanges(start=starts, end=ends)))
    o <- tapply(o[,1], o[,2], list)

    for (i in 1:length(o)) {
        pos <- as.integer(names(o)[i])
        genes.mid <- tapply(o[[i]], genes[o[[i]]], function(x, midpt) {
			       return(ind[x[which.min(abs(off[x]-midpt))]])
		           }, (starts[pos]+ends[pos])/2)
		lookupTable[as.integer(names(genes.mid)),pos] <- genes.mid
    }
    return(lookupTable)
}


.scoreIntensity <- function(lookup, intensities, minProbes=1, removeZeros=FALSE, returnMatrix=FALSE, useMean=FALSE) {
	windowMeans <- function(indexes, intensities) {
	    x <- intensities[indexes]
		if(removeZeros)
		  x <- x[x != 0]
		return(mean(x))
	}
	
	if( class(lookup)=="list") {
	  useLookup = sapply(lookup, length)>=minProbes
	  temp <- sapply(lookup[useLookup], windowMeans, intensities)
	  if (useMean) return(mean(temp, na.rm=TRUE)) else return(median(temp, na.rm=TRUE))
	} else if (class(lookup)=="matrix") {
	  d <- lookup
	  for(i in 1:ncol(lookup)) {
	    d[,i] <- intensities[  lookup[,i] ]
	  }
	  if (removeZeros)
	    d[d==0] <- NA
	  if (returnMatrix)
	    return(d)
	  if (useMean) return( apply(d,2,mean,na.rm=TRUE) ) else return( apply(d,2,median,na.rm=TRUE) )
	} else {
	  stop("lookup is neither a 'list' or a 'matrix'.")
	}
}