Count a sample list against chromosome NIPTmer lists — niptmer_count_sample_list • RGenomeTester4

Native R replacement for the legacy add_rows.pl helper.

Usage

niptmer_count_sample_list(
  sample_list,
  chr_list_dir,
  chromosomes = c(as.character(seq_len(22L)), "X", "Y"),
  chr_suffix = "_cleaned_25.list",
  sample_name = NULL,
  out_file = NULL
)

Arguments

sample_list: One or more sample .list file paths.
chr_list_dir: Directory containing chromosome list files.
chromosomes: Chromosomes to count. Defaults to autosomes plus X, Y.
chr_suffix: Suffix appended to each chromosome name inside chr_list_dir.
sample_name: Optional sample names. By default names are inferred from .list file names by stripping the trailing _<k>.
out_file: Optional output TSV path.

Value

A data.frame with CHR, TOTAL, UNIQUE, GC and one column per chromosome in chromosomes.