reduceAlleleResolution: Reduce HLA alleles

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

Reduce HLA alleles

Description

reduceAlleleResolution reduce HLA allele numbers resolution.

Usage

reduceAlleleResolution(allele, resolution = 4)

Arguments

allele	Character vector with HLA allele numbers.
resolution	Number specifying desired resolution.

Details

In cases when allele number contain additional suffix their resolution can not be unambiguously reduced. These cases are returned unchanged. Function behaves in the same manner if resolution is higher than resolution of input HLA allele numbers.

NA values are accepted and returned as NA.

TODO here we give such warning when alleles have G or GG suffix (see http://hla.alleles.org/alleles/g_groups.html) "Reducing G groups alleles, major allele gene name will be used." I dond't really remember why we are doing this xd These allele numbers are processed as normal alleles (without suffix). Let me know if this warning is relevant or we could go without it. If we want to leave it lets also add text in documentation.

Value

Character vector containing reduced HLA allele numbers.

Examples

reduceAlleleResolution(c("A*01", "A*01:24", "C*05:24:55:54"), 2)

Genentech/MiDAS documentation built on Feb. 5, 2024, 11:52 a.m.