Convert STAVE multi-locus allele frequencies to single-locus frequencies

Expands STAVE variant strings with variantstring, aggregates frequencies per amino acid allele, and emits STAVE-style single-locus variant identifiers via convert_single_locus_table_to_stave().

Usage

slaf_from_stave_mlaf(mlaf, output = NULL)

Arguments

mlaf: Path to an MLAF TSV, or a data frame with the same columns. See Inputs.
output: Optional output TSV path. Default for the CLI is single_locus_allele_frequencies.tsv.

Value

A tibble with columns variant and freq (legacy STAVE conversion drops group_id, matching the original script).

Details

Inputs

mlaf: Multilocus allele frequency table (group_id, variant, freq), as a file path or data frame. See vignette("input-formats", package = "PGEcore").

Outputs

output (optional): Single-locus allele frequency TSV with columns variant and freq. If NULL, results are returned without writing. CLI default is single_locus_allele_frequencies.tsv.

Running

slaf_from_stave_mlaf(
  mlaf = "mlaf.tsv",
  output = "single_locus_allele_frequencies.tsv"
)

Rscript exec/slaf_from_stave_mlaf \
  --mlaf mlaf.tsv \
  --output single_locus_allele_frequencies.tsv

Requires the optional variantstring package (Suggests). It is not installed automatically with PGEcore.