| multiAlign {HLAtools} | R Documentation |
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 locus 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. position will be left empty if specific allele does not have a nucleotide at the input position.
Note
For internal HLAtools use.