sortAlleles - Sort allele names

Description¶

sortAlleles returns a sorted vector of strings respresenting Ig allele names. Names are first sorted by gene family, then by gene, then by allele. Duplicated genes have their alleles are sorted as if they were part of their non-duplicated counterparts (e.g. IGHV1-69D*01 comes after IGHV1-69*01 but before IGHV1-69*02), and non-localized genes (e.g. IGHV1-NL1*01) come last within their gene family.

Usage¶

sortAlleles(allele_calls, method = c("name", "position"))

Arguments¶

allele_calls

vector of strings respresenting Ig allele names.

method

string defining the method to use when sorting alleles. If "name" then sort in lexicographic order. If "position" then sort by position in the locus, as determined by the final two numbers in the gene name.

Value¶

A sorted vector of strings respresenting Ig allele names.

Examples¶

# Create a list of allele names
alleles <- c("IGHV1-69D*01","IGHV1-69*01","IGHV1-2*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 the alleles by name
sortAlleles(alleles)

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

# Sort the alleles by position in the locus
sortAlleles(alleles, method="pos")

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

See also¶

Like sortAlleles, updateAlleleNames can help format a list of allele names.