The `chr` is not handled in `callDMR`

[mmahmoudian]

I was going through the code to understand how the DMRs are calculated, and to me it seems that the chromosome information is not taken into account while calculating DMRs. The following is my understanding of the situation:

1. The callDMR calls findBumps and pass chr in line 38:

DSS/R/DMR.R

Lines 38 to 40 in afdca98

	dmrs <- findBumps(DMLresult$chr, DMLresult$pos, scores,
	cutoff=p.threshold, sep=5000, dis.merge=dis.merge,
	pct.sig=pct.sig, minCG=minCG)

2. The findBumps then calls the findRegion and pass chr:

DSS/R/DMR.R

Line 108 in afdca98

regions <- findRegion(chr, pos, sep)

3. But the findRegion function does not take into account the chromosomes:

DSS/R/DMR.R

Lines 90 to 95 in afdca98

	findRegion <- function(chr, pos, sep=1000) {
	pos.diff <- abs(c(as.integer(0), diff(pos)))
	idx.jump <- which(pos.diff>sep)
	regions <- rbind(c(1, idx.jump), c(idx.jump-1, length(pos)))
	regions
	}

I wonder if I'm missing something or the chromosome information is not handled in findRegion.