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Annotate variants with amino-acid change and predicted impact via dndscv

Source: R/variant_annotation.R
annotate_variants_aachange.Rd

Runs dndscv on the mitochondrial variants to obtain gene-level annotation of amino-acid changes and their predicted impact.

Usage

annotate_variants_aachange(variant_annotation)

Arguments

variant_annotation

A data.frame or tibble containing at least a column named Variants of the form "".

Value

The input variant_annotation, augmented with columns:

gene

Gene symbol where the variant falls.

aachange

Amino-acid change notation (e.g. p.W88C).

impact

Predicted functional impact category from dndscv.

Details

This internal function:

  1. Loads the precomputed mitochondrial CDS reference database from the redeemR package (GRCH38_MT_bioMRT_output_refcds.rda).

  2. Converts Variants ("") into the 5-column table required by dndscv using make_mutation_table.

  3. Runs dndscv() with permissive mutation limits to annotate all coding changes.

  4. Extracts and merges back the gene, aachange, and impact fields for each variant.