minimal peak Interval example

miniTest.R

# minimal example to test revised implementation

grs <- GRangesList(
    bar= GRanges(seqnames = Rle("chr1",9),
                 IRanges(
                     c(8,18,33,53,69,81,105,115,135),
                     c(14,21,39,61,73,87,111,120,153)),
                 score=c(48,7,10,8,4,15,4,4,38)),
    cat = GRanges(seqnames = Rle("chr1",8),
                  IRanges(
                      c(6,15,20,44,71,99,113,141),
                      c(10,17,34,51,78,103,124,147)),
                  score=c(54,21,14,12,21,7,32,4)),
    foo= GRanges(seqnames = Rle("chr1",5),
                 IRanges(
                     c(11,43,57,101,117),
                     c(36,49,92,109,139)),
                 score=c(49,13,13,11,5))
)

#----------------------------------------------------------#
inDat <- lapply(grs, function(x) {
    x$p.value <- 10^(score(x)/(- 1L))
    x
})

inDat <- GRangesList(inDat)

#---------------------------------------------------------#
Hit <- peakOverlapping(inDat, whichType="max")
filtByOvHit <- filterByOverlapHit(ovHit = Hit, peakset=inDat, replicate.type = "Biological", isSuffOverlap = TRUE)

#---------------------------------------------------------#
# Trivial revision for Fisher_stats
# Note : let's do not run Fisher_stats function, I'll do rewrite its implementation

DF <- DataFrame(split(filtByOvHit, filtByOvHit$query))
pvList <- as.matrix(DF$p.value)
pvList[is.na(pvList)] <- 0
#rslt <- DataFrame(subject=DF$subject, pvalue=DF$p.value)
DF$comb.pv <- apply(pvList,1,fisherCmbp)
res <- unlist(extractList(unlist(inDat, use.names = TRUE),
                          DF$subject), use.names = FALSE)
rslt <- split(res, names(res))
# use base R to remove redundant name
rslt <- lapply(rslt, unname)

# ?? How can I make above process more efficient and computationaly less expensive ? How can I resolve mysterious duplicate removal method?
# ?? why revised implementation is not expected output ??