Function reference • hlabud

All functions

amino_distance_matrix(): Get a pairwise 20x20 distance matrix for all pairs of amino acids

dosage(): Convert a set of genotype names into a dosage matrix of each residue at each position

get_hlabud_dir(): Get the name of the folder for caching downloaded IMGTHLA files

grantham: Table 1 from Grantham 1974

hla_alignments(): Get sequence alignments from IMGTHLA

hla_alleles(): Get a table of allele names for a particular IMGTHLA release

hla_divergence(): Calculate HLA divergence for each individual

hla_frequencies(): Get HLA frequences from Allele Frequency Net Database (AFND)

hla_genes(): Get HLA gene names from IMGTHLA

hla_releases(): Get the names of releases from IMGTHLA

install_hla(): Download and unpack a tarball release from IMGTHLA

read_alignments(): Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA