uniAlign {HLAtools} | R Documentation |
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.