customAlign {HLAtools}

Generate a Customized Peptide, Codon or Nucleotide Sequence Alignment.

Description

Generates a peptide, codon, coding or genomic nucleotide alignment table for user-specified HLA alleles at user-specified positions.

Usage

customAlign(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

Either a vector of variant positions, against which all loci will be aligned, or 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 names and the corresponding nucleotide sequences for each desired nucleotide position. an error message is returned if input locus is not available in the ANHIG/IMGTHLA Github Repository.

Note

This function requires that the HLAalignments object has been populated with alignments via the alignmentFull() function. C.f., customAlign("codon",c("DRB101:01","DQB102:01","DPB101:01"),c(1,2,3,7,8,9,13,14,15)) and customAlign("codon",c("DPB101:01:01:01","DQA101:01:01:01","DQB105:01:01:01"),list(19:35,1:4,6:9)).