uniAlign {HLAtools}

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 locus 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 a specific allele if input allele is not available in the ANHIG/IMGTHLA Github Repository. position will be left empty if specific allele does not have a codon at the input position.

Note

For internal HLAtools use.