Group adjacent peaks by non-overlapping windows

Group peaks into non-overlapping genomic windows of size window_size, using peak coordinates from a BED-like metadata table.

Usage

cacti_group_peak_window(
  window_size,
  file_pheno_meta,
  file_peak_group,
  file_peak_group_peaklevel
)

Arguments

window_size

Character like "50kb" (kb units) or numeric (bp).

file_pheno_meta

Path to input phenotype meta table (with header). Columns are -

• phe_chr: chromosome, with "chr" prefix (e.g. "chr1")

• phe_from: peak start (integer, < phe_to)

• phe_to: peak end (integer)

• phe_id: peak identifier (unique per row)

file_peak_group

Output path for window-level table. Columns are - group, group_chr, group_from, group_to, pid_group, n_pid_group

file_peak_group_peaklevel

Output path for peak-level table. Columns are - phe_id, phe_chr, phe_from, phe_to, group, n_pid_group

Value

Invisibly returns the grouped window-level table; writes file_peak_group.