Export Overlap Groups to BED Files — exportOverlapsToBed • gVenn

This function exports genomic overlap groups from extractOverlaps() to BED format files, creating one BED file per overlap group.

Usage

exportOverlapsToBed(
  grouped,
  output_dir = ".",
  output_prefix = "overlaps",
  with_date = TRUE,
  verbose = TRUE
)

Arguments

grouped: Genomic overlap groups from extractOverlaps() (must be GRangesList).
output_dir: A string specifying the output directory. Defaults to ".".
output_prefix: A string specifying the filename prefix. Defaults to "overlaps".
with_date: Logical (default TRUE). Whether to prepend the current date to filenames.
verbose: Logical. If TRUE, print messages. Default TRUE.

Value

Invisibly returns a character vector of file paths created.

Details

This function only works with genomic overlaps (i.e., when the input to extractOverlaps() was a GenomicOverlapResult object, resulting in a GRangesList). It does not work with set overlaps (character vectors). Each overlap group will be saved as a separate BED file with the group identifier included in the filename.