Vector-wise Range set-operations
intersect_ranges(x, y)
intersect_ranges_directed(x, y)
union_ranges(x, y)
union_ranges_directed(x, y)
setdiff_ranges(x, y)
setdiff_ranges_directed(x, y)
complement_ranges(x)
complement_ranges_directed(x)Two Ranges objects to compare.
A Ranges object
These are usual set-operations that act on the sets of the ranges represented in x and y. By default these operations will ignore any strand information. The directed versions of these functions will take into account strand for GRanges objects.
gr1 <- data.frame(seqnames = "chr1",
start = c(2,9),
end = c(7,9),
strand = c("+", "-")) %>%
as_granges()
gr2 <- data.frame(seqnames = "chr1", start = 5, width = 5, strand = "-") %>%
as_granges()
union_ranges(gr1, gr2)
#> GRanges object with 1 range and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 2-9 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
union_ranges_directed(gr1, gr2)
#> GRanges object with 2 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 2-7 +
#> [2] chr1 5-9 -
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
intersect_ranges(gr1, gr2)
#> GRanges object with 2 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 5-7 *
#> [2] chr1 9 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
intersect_ranges_directed(gr1, gr2)
#> GRanges object with 1 range and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 9 -
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
setdiff_ranges(gr1, gr2)
#> GRanges object with 1 range and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 2-4 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
setdiff_ranges_directed(gr1, gr2)
#> GRanges object with 1 range and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 2-7 +
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# taking the complement of a ranges requires annotation information
gr1 <- set_genome_info(gr1, seqlengths = 100)
complement_ranges(gr1)
#> GRanges object with 3 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 1 *
#> [2] chr1 8 *
#> [3] chr1 10-100 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome