add a mask column to a dataframe — mark_mask

Determine if any start–end regions in the segs or reads dataframe overlaps with regions in the mask file. Will add a 'mask' boolean column to the dataframe to indicate whether the region should be masked.

Usage

mark_mask_regions(
  subject_df,
  mask_f = NULL,
  mask_chr_name = "seqnames",
  subject_chr_name = "chr"
)

Arguments

subject_df: a table with chromosome, start, and end columns. Typically the reads or segs dataframe created by import_dlp_files().
mask_f: path to a mask file, see README.md ## Setup for details.
mask_chr_name: the name of the chromosomes column in the mask file. Default is "seqnames", which is the name in the provided file.
subject_chr_name: name of the chromosome column in the reads/segs table. Default is 'chr' which is what the import scripts call the column.