sortGenes: Sort V(D)J genes

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Sort V(D)J genes

Description

sortGenes sorts a vector of V(D)J gene names by either lexicographic ordering or locus position.

Usage

sortGenes(genes, method = c("name", "position"))

Arguments

genes	vector of strings representing V(D)J gene names.
method	string defining the method to use for sorting genes. One of: "name": sort in lexicographic order. Order is by family first, then gene, and then allele. "position": sort by position in the locus, as determined by the final two numbers in the gene name. Non-localized genes are assigned to the highest positions.

Value

A sorted character vector of gene names.

See Also

See getAllele, getGene and getFamily for parsing gene names.

Examples

# Create a list of allele names
genes <- c(
    "IGHV1-69D*01", "IGHV1-69*01", "IGHV4-38-2*01", "IGHV1-69-2*01",
    "IGHV2-5*01", "IGHV1-NL1*01", "IGHV1-2*01,IGHV1-2*05",
    "IGHV1-2", "IGHV1-2*02", "IGHV1-69*02"
)

# Sort genes by name
sortGenes(genes)

# Sort genes by position in the locus
sortGenes(genes, method = "pos")

alakazam documentation built on Nov. 5, 2025, 6:55 p.m.