generateReferenceSet - Generate allele similarity reference set

Description¶

Generates the allele clusters reference set based on the clustering from ighvClust. The function collapse similar alleles and assign them into their respective allele clusters and family clusters. See details for naming scheme

Usage¶

generateReferenceSet(germline_distance, germline_set, alleleClusterTable)

Arguments¶

germline_distance

A germline set distance matrix created by ighvDistance.

germline_set

A character list of the IMGT aligned IGHV allele sequences. See details for curating options.

alleleClusterTable

A data.frame of the alleles and their clusters created by ighvClust.

Value¶

A list with the re-named germline set, and a table of the allele clusters and thresholds.

Details¶

Each allele is named by this scheme: IGHVF1-G1*01 - IGH = chain, V = region, F1 = family cluster numbering, G1 - allele cluster numbering, and 01 = allele numbering (given by clustering order, no connection to the expression)