Hi,

I am trying to create a redundant list from two different lists of
chromosomal ranges as follow:

*List 1:*
   Chr Start Stop  chr1 0 98595  chr1 17012368 17012439  chr1 17017304
17029919  chr1 17246620 17250887
*List 2:*
   Chr Start Stop  chr1 82483 98595  chr1 17225296 17232195  chr1 17235775
17236214  chr1 17246096 17257401


>From these two lists, I want to create one list by (i) intersecting the
regions if they overlap between two lists but (ii) also keeping the ones
unique in either of the lists. So far, I can do the intersection using
GRanges (suggested by Martin Morgan) but can not get the unique regions
only present in either groups. I am using the folowing code:

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
library(GenomicRanges)
rel=read.csv('file1.csv', header=T, sep=',')
nonrel=read.csv(file2.csv', header=T, sep=',')
subject=GRanges(rel$Chr, IRanges(rel$Start, rel$Stop))
Query=GRanges(nonrel$Chr, IRanges(nonrel$Start, nonrel$Stop))
result=as.data.frame(intersect (subject,Query))
write.table(result, file='Result.csv', sep=',')

Could anyone tell me how to insert a piece of code to keep the unique
regions in either of the lists?

Regards,
--Yadav

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