9 months ago by

United States

Do note that you cannot really have a matrix showing the overlap between the three `GRanges`

objects, because there will be different regions defined in the three `GRanges`

. Instead, you could define a common set of genomic ranges and then make an incidence matrix showing if a given range in a particular `GRanges`

object overlaps.

```
> gr.1 <- regioneR::createRandomRegions(nregions=1000, length.mean=500000, length.sd=30000)
> gr.2 <- regioneR::createRandomRegions(nregions=1000, length.mean=500000, length.sd=30000)
> gr.3 <- regioneR::createRandomRegions(nregions=1000, length.mean=500000, length.sd=30000)
> base <- reduce(c(gr.1, gr.2, gr.3))
> base
GRanges object with 2096 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 729836-1633109 *
[2] chr1 1946672-2419469 *
[3] chr1 2952076-3463275 *
[4] chr1 3836898-4273778 *
[5] chr1 4931353-6065223 *
... ... ... ...
[2092] chr6_qbl_hap6 3481669-4494167 *
[2093] chr6_ssto_hap7 717078-1631256 *
[2094] chr6_ssto_hap7 3139239-3635135 *
[2095] chr17_ctg5_hap1 154779-591672 *
[2096] chr17_ctg5_hap1 978830-1633449 *
-------
seqinfo: 93 sequences from an unspecified genome; no seqlengths
> z <- matrix(0,length(base),3)
> z[subjectHits(findOverlaps(gr.1, base)),1] <- 1
> z[subjectHits(findOverlaps(gr.2, base)),2] <- 1
> z[subjectHits(findOverlaps(gr.3, base)),3] <- 1
> colnames(z) <- paste0("gr.", 1:3)
> mcols(base) <- z
> base
GRanges object with 2096 ranges and 3 metadata columns:
seqnames ranges strand | gr.1 gr.2 gr.3
<Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric>
[1] chr1 729836-1633109 * | 0 1 1
[2] chr1 1946672-2419469 * | 0 1 0
[3] chr1 2952076-3463275 * | 0 1 0
[4] chr1 3836898-4273778 * | 0 1 0
[5] chr1 4931353-6065223 * | 0 1 1
... ... ... ... . ... ... ...
[2092] chr6_qbl_hap6 3481669-4494167 * | 1 1 0
[2093] chr6_ssto_hap7 717078-1631256 * | 1 1 0
[2094] chr6_ssto_hap7 3139239-3635135 * | 0 0 1
[2095] chr17_ctg5_hap1 154779-591672 * | 0 0 1
[2096] chr17_ctg5_hap1 978830-1633449 * | 1 1 0
-------
seqinfo: 93 sequences from an unspecified genome; no seqlengths
```

Is, I believe, pretty close to what you want?