Calculate single-locus allele frequencies from microhaplotype frequencies

Joins microhaplotype allele frequencies to translated amino acid calls, aggregates frequencies per amino acid allele, and renormalises so frequencies sum to one. Collapsed output averages evenly across overlapping targets (taking max(sample_total)).

Usage

slaf_from_mhaps_freqs(
  mhaps_slaf,
  loci_of_interest_per_microhaps,
  slaf_output = NULL,
  per_target_slaf_output = NULL
)

Arguments

mhaps_slaf: Path or data frame of microhaplotype SLAF. See Inputs.
loci_of_interest_per_microhaps: Path or data frame of translated loci. See Inputs.
slaf_output: Optional path for collapsed SLAF TSV.
per_target_slaf_output: Optional path for per-target SLAF TSV.

Value

A list with tibbles slaf (collapsed) and per_target_slaf.

Details

Inputs

mhaps_slaf: Microhaplotype SLAF (target_name, seq, freq, sample_total), as a file path or data frame. See vignette("input-formats", package = "PGEcore").
loci_of_interest_per_microhaps: Translated loci per microhaplotype (target_name, gene_id, aa_position, seq, aa), as a file path or data frame.

Outputs

slaf_output (optional): Collapsed SLAF TSV (variant, freq, sample_total).
per_target_slaf_output (optional): Per-target SLAF TSV (target_name, variant, freq, sample_total).

Running

slaf_from_mhaps_freqs(
  mhaps_slaf = "mhaps_slaf.tsv",
  loci_of_interest_per_microhaps = "loci_of_interest_per_microhaps.tsv",
  slaf_output = "slaf.tsv"
)

Rscript exec/slaf_from_mhaps_freqs \
  --mhaps_slaf mhaps_slaf.tsv \
  --loci_of_interest_per_microhaps loci_of_interest_per_microhaps.tsv \
  --slaf_output slaf.tsv