filterPeak: Filter Peak Sets
In qwang-big/irene: R interface to interactive epigenetic analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Filter peak sets with reference genomic regions

1	filterPeak(files, ref, group, data, filter)

`files`	Vector of filenames of the peak sets used to filter the reference genomic regions.
`ref`	Data.frame of reference genomic regions needed to be filtered.
`group`	Vector of groups used to combine the regions, this must be of the same length to the vector of filenames. If groups is set to NULL, `combineRgn` will be called instead of `combineGrpRgn`.
`data`	Data.frame or matrix which contains the intensity data for each input genomic regions. If provided, the function further discards the genomic regions having zero-variance between groups.
`filter`	Vector of which type of genomic regions to filter, the value must be one of "enhancer", "promoter" or "both".

This function combines peak sets with or without group information, then findOverlaps will be called to get IDs of the overlaps, and intersect with the IDs of the reference genomic regions.

Vector of indices of overlapped reference genomic regions.

Qi Wang

combineRgn, combineGrpRgn, filterRgn

testBed <- tempfile()
control <- tempfile()
enhancer <- data.frame(chr="chr1", start=c(1,4,7,10), end=c(2,5,8,11), id=c("GH123456789","GH987654321","prom_1","prom_2"), stringsAsFactors=FALSE)
write.table(data.frame(chr="chr1", start=c(1,4,7), end=c(2,5,8)), testBed, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
write.table(data.frame(chr="chr1", start=c(1,7,10), end=c(2,8,11)), control, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
i <- filterPeak(c(testBed,control),enhancer,group=1:2,filter="enhancer")