On 03/04/2012 11:06 AM, Yadav Sapkota wrote:
Hi,
I want to merge multiple chromosomal regions based on their common
intersecting regions. I tried couple of things using while and if loops but
did not work out.
I would appreciate if anyone could provide me a small piece of code in R to
get the intersection of following example:
chr1: 100-150
chr1: 79-250
chr1: 100-175
chr1: 300-350
I want the intersection of all four regions as follow:
chr1: 100-150
chr1: 300-350
I have thousands of these regions (some overlap and some not).
Not exactly sure what you mean by 'intersection of all four regions' but
source("http://bioconductor.org/biocLite.R";)
biocLite("GenomicRanges")
and then
library(GenomicRanges)
q = GRanges("chr1", IRanges(c(100, 79, 100, 300),
c(150, 250, 175, 350)))
s = GRanges("chr1", IRanges(c(100, 300),
c(150, 350)))
o = findOverlaps(query=q, subject=s)
xtabs(~queryHits(o) + subjectHits(o))
leading to
subjectHits(o)
queryHits(o) 1 2
1 1 0
2 1 0
3 1 0
4 0 1
This will be efficient for (10's of) millions of overlaps. There are
extensive vignettes for help, vignettes(package="IRanges"),
vignettes(package="GenomicRanges") and the Bioconductor mailing list
http://bioconductor.org/help/mailing-list/
is the appropriate place for further help in this direction.
Martin
Regards,
--Yadav
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