alakazam (version 1.4.0)

sortGenes: 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"))

Value

A sorted character vector of gene names.

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.

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")