Per-locus nucleotide diversity, segregating sites, and Tajima's D

Groups allele sequences by locus and computes population-genetic summaries.

Usage

per_locus_popgen_summary(
  allele_table,
  specimen_name_col = "specimen_name",
  target_name_col = "target_name",
  target_value_col = "seq",
  output = "per_locus_popgen_summary.tsv",
  msa_method = "Muscle"
)

Arguments

allele_table: Path to an allele table TSV. See Inputs.
specimen_name_col: Specimen ID column name.
target_name_col: Locus column name.
target_value_col: Allele/sequence column name.
output: Optional output TSV path. Defaults to "per_locus_popgen_summary.tsv".
msa_method: Alignment method: "Muscle" (default), "ClustalW", or "ClustalOmega".

Value

A tibble of per-locus statistics with lower-case column names.

Details

Inputs

allele_table: Allele table (default columns specimen_name, target_name, seq). See vignette("input-formats", package = "PGEcore").

Outputs

output (optional): Per-locus stats TSV with lower-case column names (e.g. target_name, nucleotide_diversity, segregating_sites, tajima_d, …). Defaults to "per_locus_popgen_summary.tsv". If NULL, results are returned without writing.

Running

per_locus_popgen_summary(
  allele_table = "allele_table.tsv",
  output = "per_locus_popgen_summary.tsv"
)

Rscript exec/per_locus_popgen_summary \
  --allele_table allele_table.tsv \
  --output per_locus_popgen_summary.tsv

Requires ape, msa, and pegas (Suggests). msa calls an external aligner; install the binary for msa_method on PATH:

"Muscle" — muscle
"ClustalW" — clustalw
"ClustalOmega" — clustalo