validate_aac_ids: Ensure AAC IDs are valid for a given reference data set

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

Ensure AAC IDs are valid for a given reference data set

Description

Given a vector of AAC IDs, determines whether each is valid/possible, returning NULL if all are valid, or a list of problems, or an error if input isn't parseable.

Usage

validate_aac_ids(aac_ids, refset)

Arguments

aac_ids	AAC variant IDs
refset	reference data set (environment object)

Details

An ID is invalid if the gene and/or protein_id are not in the reference data, or if the reference amino acid ("G" in KRAS_G12C) is incorrect, or if there is no possible SNV that can create the proposed change. For example, KRAS G12C is possible when the codon (GGT) acquires a G>T substitution in the first position, while G12K is not possible because no single substitution can transform GGT into a lysine codon.

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.