reassignAlleles - Correct allele calls based on a personalized genotype

Description

reassignAlleles uses a subject-specific genotype to correct correct preliminary allele assignments of a set of sequences derived from a single subject.

Usage

reassignAlleles(data, genotype_db, v_call = "V_CALL",
seq = "SEQUENCE_IMGT", method = "hamming", path = NA,
keep_gene = c("gene", "family", "repertoire"))

Arguments

data
a data.frame containing V allele calls from a single subject and the sample IMGT-gapped V(D)J sequences under "SEQUENCE_IMGT".
genotype_db
a vector of named nucleotide germline sequences matching the calls detailed in allele_calls and personalized to the subject
v_call
name of the column in data with V allele calls. Default is "V_CALL".
seq
name of the column in data with the aligned, IMGT-numbered, V(D)J nucleotide sequence. Default is SEQUENCE_IMGT
method
the method to be used when realigning sequences to the genotype_db sequences. Currently, only "hammming" (for Hamming distance) is implemented.
path
directory containing the tool used in the realignment method, if needed. Hamming distance does not require a path to a tool.
keep_gene
a string indicating if the gene ("gene"), family ("family") or complete repertoire ("repertoire") assignments should be performed. Use of "gene" increases speed by minimizing required number of alignments, as gene level assignments will be maintained when possible.

Value

A modifed input data.frame containing the best allele call from among the sequences listed in genotype_db in the V_CALL_GENOTYPED column.

Details

In order to save time, initial gene assignments are preserved and the allele calls are chosen from among those provided in genotype_db, based on a simple alignment to the sample sequence.

Examples

# Extract the database sequences that correspond to the genotype
genotype_db <- genotypeFasta(SampleGenotype, SampleGermlineIGHV, novel=SampleNovel)

# Use the personlized genotype to determine corrected allele assignments
output_db <- reassignAlleles(SampleDb, genotype_db)