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Annotate variant table with population frequency and haplogroup statistics

Source: R/variant_annotation.R
annotate_variants_population_stats.Rd

Adds mitochondrial variant information from mitomap_freq and haplogroup marker counts from haplogroup_markers to a variant annotation table. Existing columns that would collide with the annotation fields are removed before the joins are applied.

Usage

annotate_variants_population_stats(variant_annotation)

Arguments

variant_annotation

A data.frame or tibble containing at least columns Variants and CellN.

Value

The input variant_annotation with population-frequency, RSRS50, and haplogroup marker-count columns added.

Details

The added fields include:

  • Locus: gene, tRNA, or other mitochondrial feature.

  • RSRS50: ancestral-state flag.

  • freq_all, freq_african, freq_asian, freq_eurasian: MITOMAP population-frequency summaries.

  • n_haplos: number of haplogroup marker entries for the variant.