Sort V(D)J genes

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Description

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

Usage

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

Arguments

genes

vector of strings respresenting 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

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# 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")

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