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"))

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.

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)

 [1] "IGHV1-2"               "IGHV1-2*01,IGHV1-2*05" "IGHV1-2*02"           
 [4] "IGHV1-69*01"           "IGHV1-69D*01"          "IGHV1-69*02"          
 [7] "IGHV1-69-2*01"         "IGHV1-NL1*01"          "IGHV2-5*01"           
[10] "IGHV4-38-2*01"        

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

 [1] "IGHV1-NL1*01"          "IGHV1-69-2*01"         "IGHV1-69*01"          
 [4] "IGHV1-69D*01"          "IGHV1-69*02"           "IGHV4-38-2*01"        
 [7] "IGHV2-5*01"            "IGHV1-2"               "IGHV1-2*01,IGHV1-2*05"
[10] "IGHV1-2*02"           

See also¶

See getAllele, getGene and getFamily for parsing gene names.