validateAllele {HLAtools}

Validate Allele-Name Format and Presence in HLAalignments

Description

Returns TRUE if an allele name is found in HLAalignments in either the 'allele_name' column of full-length allele names or the 'trimmed_allele' column of two-field allele names in the pertinent genomic alignment. Returns FALSE if the allele name is not properly formed, or if the allele name is not found in HLAalignments.

Usage

validateAllele(allele)

Arguments

allele

A character string of the colon-delimited HLA allele name.

Value

A logical identifying if the allele name is present in the alignments (TRUE) or, if it is not in the alignments or is not valid not (FALSE).

Note

Messages will be returned to the console if the allele name is malformed, or the locus is invalid; e.g., validateAllele("C01:01:01:01") or validateAllele("A01:01:01:01:01").

The locus being evaluated must be included in HLAalignments.