I would like to find overlapped regions in the file and merge them keeping the earlier start and the later stop (merge 2 regions in 1)
I meant to use Genomic Ranges but I am not sure how to code the script.
This is what the file fileA.txt contain:
chr start end value
chr1 58708485 58708713 1
chr1 58709084 58710538 2
chr1 98766295 98766639 3
chr1 98766902 98770338 4
Script:
library(GenomicRanges)
query = with(fileA.txt, GRanges(chr, IRanges(start=start, end=end)))
subject = with(fileA.txt, GRanges(chr, IRanges(start=start, end=end)))
hits = findOverlaps(gr1)
ranges(query)[queryHits(hits)] = ranges(subject)[subjectHits(hits)]
I am not sure how to set query and subject for a single file, as well the object being a document need any kind of "" or specific format (bedGraph, txt are fine?) in order to be recognised in the script?
Thank you a lot in advance for your help!
K.
