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Write Haplotype Character (Nucleotide) Matrix

Source: R/haplotypes.R
write_haplotype_character.Rd

Writes a matrix where each cell contains the nucleotide sequence of the haplotype allele carried by each individual. Rows are haplotype alleles, columns are individuals. This is the most interpretable format: you can read directly which nucleotides define each haplotype allele and which individuals carry it.

Usage

write_haplotype_character(
  haplotypes,
  snp_info,
  out_file,
  min_freq = 0.01,
  top_n = NULL,
  missing_string = ".",
  verbose = TRUE
)

Arguments

haplotypes

List from extract_haplotypes.

snp_info

Data frame with SNP, CHR, POS, REF, ALT.

out_file

Output file path (tab-delimited).

min_freq

Minimum haplotype frequency. Default 0.01.

top_n

Integer or NULL. Cap alleles per block. NULL (default) keeps all above min_freq.

missing_string

Missing genotype marker. Default ".".

verbose

Logical. Default TRUE.

Value

Invisibly returns out_file.

Details

The cell value for individual i at haplotype allele h is:

  • The nucleotide sequence (e.g. "AGTTA") if the individual carries that allele (dosage = 2 for unphased, or present in either gamete for phased).

  • "-" if the individual does not carry that allele.

  • "." if the individual has missing data in that block.

Heterozygous positions (dosage = 1, phased data only) are encoded using IUPAC ambiguity codes: R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C. This keeps the nucleotide string the same length as n_snps regardless of how many heterozygous positions are present.