Extend genome ranges in a strand-aware fashion.

Usage

extend_ranges(
  ranges,
  upstream = 0,
  downstream = 0,
  metadata_cols = c("strand"),
  chromosome_sizes = NULL,
  zero_based_coords = !is(ranges, "GRanges")
)

Arguments

ranges

Genomic regions given as GRanges, data.frame, or list. See help("genomic-ranges-like") for details on format and coordinate systems. Required attributes:

chr, start, end: genomic position

upstream

Number of bases to extend each range upstream (negative to shrink width)

downstream

Number of bases to extend each range downstream (negative to shrink width)

metadata_cols

Optional list of metadata columns to require & extract

chromosome_sizes

(optional) Size of chromosomes as a genomic-ranges object

zero_based_coords

If true, coordinates start and 0 and the end coordinate is not included in the range. If false, coordinates start at 1 and the end coordinate is included in the range

Details

Note that ranges will be blocked from extending past the beginning of the chromosome (base 0), and if chromosome_sizes is given then they will also be blocked from extending past the end of the chromosome