Find overlaps within a Ranges object
join_overlap_self(x, maxgap, minoverlap)
join_overlap_self_within(x, maxgap, minoverlap)
join_overlap_self_directed(x, maxgap, minoverlap)
join_overlap_self_within_directed(x, maxgap, minoverlap)A Ranges object
The maximimum gap between intervals as an integer greater than or equal to zero. The minimum amount of overlap between intervals as an integer greater than zero, accounting for the maximum gap.
a Ranges object
Self overlaps find any overlaps (or overlaps within or overlaps directed) between a ranges object and itself.
query <- data.frame(start = c(5,10, 15,20), width = 5, gc = runif(4)) %>%
as_iranges()
join_overlap_self(query)
#> IRanges object with 4 ranges and 2 metadata columns:
#> start end width | gc gc.overlap
#> <integer> <integer> <integer> | <numeric> <numeric>
#> [1] 5 9 5 | 0.0410528 0.0410528
#> [2] 10 14 5 | 0.3613966 0.3613966
#> [3] 15 19 5 | 0.5709781 0.5709781
#> [4] 20 24 5 | 0.6848802 0.6848802
# -- GRanges objects, strand is ignored by default
query <- data.frame(seqnames = "chr1",
start = c(11,101),
end = c(21, 200),
name = c("a1", "a2"),
strand = c("+", "-"),
score = c(1,2)) %>%
as_granges()
# ignores strandedness
join_overlap_self(query)
#> GRanges object with 2 ranges and 4 metadata columns:
#> seqnames ranges strand | name score name.overlap
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character>
#> [1] chr1 11-21 + | a1 1 a1
#> [2] chr1 101-200 - | a2 2 a2
#> score.overlap
#> <numeric>
#> [1] 1
#> [2] 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
join_overlap_self_within(query)
#> GRanges object with 2 ranges and 4 metadata columns:
#> seqnames ranges strand | name score name.overlap
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character>
#> [1] chr1 11-21 + | a1 1 a1
#> [2] chr1 101-200 - | a2 2 a2
#> score.overlap
#> <numeric>
#> [1] 1
#> [2] 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# adding directed prefix includes strand
join_overlap_self_directed(query)
#> GRanges object with 2 ranges and 4 metadata columns:
#> seqnames ranges strand | name score name.overlap
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character>
#> [1] chr1 11-21 + | a1 1 a1
#> [2] chr1 101-200 - | a2 2 a2
#> score.overlap
#> <numeric>
#> [1] 1
#> [2] 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths