R: Sort V(D)J genes

sortGenes {alakazam} | R Documentation

## 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 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

    # 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")

[Package alakazam version 0.3.0 Index]