Write Haplotype Feature Matrix as Numeric Dosage Table — write_haplotype

Writes the haplotype dosage matrix in a tab-delimited format with haplotype alleles as rows and individuals as columns. Metadata columns (hap_id, CHR, start_bp, end_bp, n_snps, alleles, frequency) precede the individual columns. Individual cells contain 0/1/2/NA dosage values.

Usage

write_haplotype_numeric(
  hap_matrix,
  out_file,
  haplotypes = NULL,
  snp_info = NULL,
  hap_info = NULL,
  sep = "\t",
  na_str = "NA",
  min_freq = 0.01,
  missing_string = ".",
  verbose = TRUE
)

Arguments

hap_matrix: Numeric matrix (individuals x haplotype alleles) from build_haplotype_feature_matrix.
out_file: Output file path.
haplotypes: List from extract_haplotypes. When supplied together with snp_info, the alleles and frequency metadata columns are populated.
snp_info: Data frame with CHR, POS, REF, ALT. Required for alleles column.
hap_info: Data frame of exact per-column metadata from build_haplotype_feature_matrix()\$info. When supplied, the alleles, frequency, n_snps, CHR, start_bp, and end_bp columns are written directly from this object without any reconstruction. Recommended - pass hap_info = feat_out\$info where feat_out is the return value of build_haplotype_feature_matrix(). Default NULL (falls back to legacy reconstruction from haplotypes and snp_info).
sep: Field separator. Default ",".
na_str: NA string. Default "NA".
min_freq: Minimum frequency used when computing alleles. Default 0.01.
missing_string: Missing genotype marker. Default ".".
verbose: Logical. Default TRUE.

Value

Invisibly returns out_file.