multiAlign: Generate an Alignment for Specific Alleles at Different...

In HLAtools: Toolkit for HLA Immunogenomics

Generate an Alignment for Specific Alleles at Different Positions

Description

Generates a peptide, codon, coding nucleotide or genomic alignment for HLA alleles, allowing each allele to be aligned to a different set of positions.

Usage

multiAlign(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 list of vectors of nucleotide positions, exactly one vector for each allele, against which each corresponding allele will be aligned.

Value

A data frame of 'allele' and the corresponding nucleotide sequence for specified positions designated for an allele. A nucleotide sequence is not returned for a specific allele if input allele is not available in the ANHIG/IMGTHLA Github Repository. A position will be left empty if the specific allele does not have a variant at that 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.