sort_and_validate_variant_ids: Sort and validate input variant IDs

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

Sort and validate input variant IDs

Description

Sorts input variant IDs by type, completes IDs by adding protein ID to plain variant names (e.g. "KRAS G12C"), and ensures that IDs are valid even if not present in annotations. This includes verifying that reference alleles are correct in SNV IDs and that amino acid changes are possible given the coding sequence.

Usage

sort_and_validate_variant_ids(cesa, input_ids, drop_unannotated = FALSE)

Arguments

cesa	CESAnalysis
input_ids	Variant names/IDs, typically from user.
drop_unannotated	Whether to include variants that are not annotated in output.

Value

List of variant_ids, with each element corresponding to one variant_type.

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