updateAlleleNames: Update IGHV allele names

In tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data

Update IGHV allele names

Description

updateAlleleNames takes a set of IGHV allele calls and replaces any outdated names (e.g. IGHV1-f) with the new IMGT names.

Usage

updateAlleleNames(allele_calls)

Arguments

allele_calls

vector of strings respresenting IGHV allele names.

Value

Vector of strings respresenting updated IGHV allele names.

Note

IGMT has removed IGHV2-5*10 and IGHV2-5*07 as it has determined they are actually alleles 02 and 04, respectively. The updated allele names are based on IMGT release 2014-08-4.

References

1. Xochelli et al. (2014) Immunoglobulin heavy variable (IGHV) genes and alleles: new entities, new names and implications for research and prognostication in chronic lymphocytic leukaemia. Immunogenetics. 67(1):61-6

See Also

Like updateAlleleNames, sortAlleles can help format a list of allele names.

Examples

# Create a vector that uses old gene/allele names.
alleles <- c("IGHV1-c*01", "IGHV1-f*02", "IGHV2-5*07")

# Update the alleles to the new names
updateAlleleNames(alleles)

tigger documentation built on Oct. 10, 2023, 5:08 p.m.