I need to find length of overlapped region on same chromosomes between 2 group(gp1 & gp2). (similar question in stackoverflow were different from my aim, because I wanna find overlapped region not a TRUE/FALSE answer).
For example:
gp1:
chr start end id1
chr1 580 600 1
chr1 900 970 2
chr3 400 600 3
chr2 100 700 4
gp2:
chr start end id2
chr1 590 864 1
chr3 550 670 2
chr2 897 1987 3
I'm looking for a way to compare these 2 group and get results like this:
id1 id2 chr overlapped_length
1 1 chr1 10
3 2 chr3 50
Should point you in the right direction:
# install.packages("BiocManager")
# BiocManager::install("GenomicRanges")
library(GenomicRanges)
library(IRanges)
gp1 <- read.table(text =
"
chr start end id1
chr1 580 600 1
chr1 900 970 2
chr3 400 600 3
chr2 100 700 4
", header = TRUE)
gp2 <- read.table(text =
"
chr start end id2
chr1 590 864 1
chr3 550 670 2
chr2 897 1987 3
", header = TRUE)
gr1 <- GenomicRanges::makeGRangesFromDataFrame(
gp1,
seqnames.field = "chr",
start.field = "start",
end.field = "end"
)
gr2 <- GenomicRanges::makeGRangesFromDataFrame(
gp2,
seqnames.field = "chr",
start.field = "start",
end.field = "end"
)
hits <- findOverlaps(gr1, gr2)
p <- Pairs(gr1, gr2, hits = hits)
i <- pintersect(p)
> as.data.frame(i)
seqnames start end width strand hit
1 chr1 590 600 11 * TRUE
2 chr3 550 600 51 * TRUE