uniAlign: Generate an Alignment for Specific Alleles at Specific...

In HLAtools: Toolkit for HLA Immunogenomics

Generate an Alignment for Specific Alleles at Specific Positions

Description

Generates a peptide, codon, coding or genomic nucleotide alignment at a single set of positions for HLA alleles at one or more loci.

Usage

uniAlign(alignType, alleles, positions)

Arguments

alignType	The type of alignment being searched. Allowed values are "prot", codon", "nuc" and "gen". Only one 'alignType' value is allowed.
alleles	A vector of un-prefixed HLA allele names.
positions	A vector of codon positions, against which all loci will be aligned.

Value

A data frame of allele names and the corresponding codon sequence for specified position. A codon sequence is not returned for alleles that are not present in the loaded HLAalignments object. A sequence position will be populated with whitespace if a specific allele has no sequence at the specified position. If 'positions' includes values that do not exist in the specified alignment, FALSE is returned.

Note

For internal HLAtools use.

HLAtools documentation built on June 8, 2025, 12:24 p.m.