Hello everyone

I'm trying to select the interactions that lie inside of a given region, but my problem is that this doesn't work properly because it gives me interactions that one anchor of the interactions lies outside of the given region.

I prepared a toy example, there are 2 interactions and one given region. The second interaction starts inside the region but finishes outside the region, so subsetByOverlaps with the argument type="within" should filter out this interaction, but it doesn't.

a1 <-  GRanges(seqnames = 1,ranges = IRanges(start = c(100,150),end = c(110,160)))
a2 <-  GRanges(seqnames = 1,ranges = IRanges(start = c(200,250),end = c(210,260)))
gi <- GenomicInteractions(a1,a2)

region <- GRanges(seqnames = 1,raenter code herenges = IRanges(start = 1,end = 230))

subsetByOverlaps(gi,region,type = "within")
# GenomicInteractions object with 2 interactions and 1 metadata column:
#   seqnames1   ranges1     seqnames2   ranges2 |    counts
#       <Rle> <IRanges>         <Rle> <IRanges> | <integer>
# [1]       1   100-110 ---         1   200-210 |         1
# [2]       1   150-160 ---         1   250-260 |         1
# -------
#   regions: 4 ranges and 0 metadata columns
# seqinfo: 1 sequence from an unspecified genome; no seqlengths

If I apply separately subsetByOverlaps to the regions of each anchor, it works, but when I try to do it to the GenomicInteractions object it doesn't.

Is this a bug or how can I solve this and obtained only the interactions that really lie inside the region?

Thanks