hlaToAAVariation: Generate amino acid variation matrix

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

Generate amino acid variation matrix

Description

hlaToAAVariation convert HLA calls data frame to a matrix of variable amino acid positions.

Usage

hlaToAAVariation(hla_calls, indels = TRUE, unkchar = FALSE, as_df = TRUE)

Arguments

hla_calls	HLA calls data frame, as returned by readHlaCalls function.
indels	Logical indicating whether indels should be considered when checking variability.
unkchar	Logical indicating whether unknown characters in the alignment should be considered when checking variability.
as_df	Logical indicating if data frame should be returned. Otherwise a matrix is returned.

Details

Variable amino acid positions are found by comparing elements of the alignment column wise. Some of the values in alignment can be treated specially using indels and unkchar arguments. Function processes alignments for all HLA genes found in hla_calls.

Variable amino acid position uses protein alignments from EBI database.

Value

Matrix or data frame containing variable amino acid positions. Rownames corresponds to ID column in hla_calls, and colnames to alignment positions. If no variation is found one column matrix filled with NA's is returned.

Examples

hlaToAAVariation(MiDAS_tut_HLA)

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