Fragments can be subset based on overlapping (or not overlapping) a set of regions
Usage
select_regions(
fragments,
ranges,
invert_selection = FALSE,
zero_based_coords = !is(ranges, "GRanges")
)Arguments
- fragments
Input fragments object.
- ranges
Peaks/ranges to overlap, 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
- invert_selection
If TRUE, select fragments not overlapping selected regions instead of only fragments overlapping the selected regions.
- zero_based_coords
Whether to convert the ranges from a 1-based end-inclusive coordinate system to a 0-based end-exclusive coordinate system. Defaults to true for GRanges and false for other formats (see this archived UCSC blogpost)
