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
generateReferenceSet(
germline_distance,
germline_set,
alleleClusterTable,
trim_3prime_side = NULL
)A list with the re-named germline set, and a table of the allele clusters and thresholds.
A germline set distance matrix created by ighvDistance.
A character list of the IMGT aligned IGHV allele sequences. See details for curating options.
A data.frame of the alleles and their clusters created by ighvClust.
If a 3' position trim is supplied, duplicated sequences will be checked for differential positions past the trim position. Default NULL; NULL will not activate the check. see @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)
In case there are alleles that are differentiated in a nucleotide position past the trimming position used for the clustering, then the alleles are separated and are annotated with the differentiating position as so: Say A101 and A102 are similar up to position 318, and thus collapsed in the clusters to G101. Upon checking the sequences past the trim position (318), a differentiating nucleotide was seen in position 319, A101 has a G, and A102 has a T. Then the alleles will be separated, and the new annotation will be as so: A101 = G101, and A102 = G1*01_G319T. Where the first nucleotide indicate the base, the following number the position, and the last nucleotide the one the base changed into.