summariseAAPosition: Summarize amino acid position

In Genentech/midasHLA: R package for immunogenomics data handling and association analysis

Summarize amino acid position

Description

List HLA alleles and amino acid residues at a given position.

Usage

summariseAAPosition(hla_calls, aa_pos, aln = NULL, na.rm = FALSE)

Arguments

hla_calls	HLA calls data frame, as returned by readHlaCalls function.
aa_pos	String specifying gene and amino acid position, example "A_9".
aln	Matrix containing amino acid sequence alignments as returned by readHlaAlignments function. By default function will use alignment files shipped with the package.
na.rm	Logical flag indicating if NA values should be considered for frequency calculations.

Value

Data frame containing HLA alleles, their corresponding amino acid residues and frequencies at requested position.

Examples

summariseAAPosition(MiDAS_tut_HLA, "A_9")

Genentech/midasHLA documentation built on Feb. 12, 2024, 9:38 a.m.