validatePositions: Validate the Presence of Variant Positions in an Alignment

In HLAtools: Toolkit for HLA Immunogenomics

Validate the Presence of Variant Positions in an Alignment

Description

Returns TRUE when variant positions are present in a specified alignment in HLAalignments. Returns false when any variant position is not present in the specified alignment and generates a message identifying such positions.

Usage

validatePositions(alignType, locus, positions)

Arguments

alignType	The type of alignment being searched. Allowed values are "prot", codon", "nuc" and "gen". Only one 'alignType' value is allowed.
locus	A locus supported by the IPD-IMGT/HLA Database.
positions	A vector of variant positions.

Value

A logical identifying if the position is present in the alignment (TRUE) or, if it is not in the alignment or is not valid (FALSE).

Note

For internal HLAtools use.

HLAtools documentation built on June 8, 2025, 12:24 p.m.