compareSequences {HLAtools}

Identify Sequence Differences Between Two Alleles at a Locus

Description

Compares the sequences of two alleles at a locus, and identifies the differences between them at specific positions

Usage

compareSequences(alignType, alleles)

Arguments

alignType

A character string identifying the type of alignment being searched. Allowed values are "codon","gen", nuc" and "prot". Only one 'alignType' value is permitted.

alleles

A character vector containing two full-length names for alleles at the same locus.

Value

A two-row data frame identifying the positions and sequences at which the two alleles differ. E.g., compareSequences(alignType = "gen", alleles = c("DPA101:03:38:01","DPA101:03:38:02"). Positions for which the sequence of either allele is unknown are ignored.