Stitch Ranges within a given distance

Stitch together ranges within a given distance, using excluded ranges as barriers that cannot be crossed

stitchRanges(x, exclude, maxgap = 12500L, ignore.strand = TRUE)

Arguments

x

Ranges to be stitched together

exclude

Ranges to exclude

maxgap

The maximum distance between ranges to be stitched

ignore.strand

logical

Value

A GRanges object

Details

Stitches together ranges within a given distance, using any ranges provided for exclusion as barriers between stitched ranges. This may be particularly useful if wanting to stitch enhancers whilst excluding promoters.

All inputs and outputs are Genomic Ranges objects

Examples

x <- GRanges(c("chr1:1-10", "chr1:101-110", "chr1:201-210", "chr2:1-10"))
y <- GRanges("chr1:200:+")
stitchRanges(x, exclude = y, maxgap = 100)
#> GRanges object with 3 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1     1-110      *
#>   [2]     chr1   201-210      *
#>   [3]     chr2      1-10      *
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths