reassignAlleles - Correct allele calls based on a personalized genotype
reassignAlleles uses a subject-specific genotype to correct
correct preliminary allele assignments of a set of sequences derived
from a single subject.
reassignAlleles(data, genotype_db, v_call = "V_CALL", method = "hamming", path = NA, keep_gene = c("gene", "family", "repertoire"))
data.framecontaining V allele calls from a single subject and the sample IMGT-gapped V(D)J sequences under
- a vector of named nucleotide germline sequences
matching the calls detailed in
allele_callsand personalized to the subject
- name of the column in
datawith V allele calls. Default is
- the method to be used when realigning sequences to
the genotype_db sequences. Currently, only
"hammming"(for Hamming distance) is implemented.
- directory containing the tool used in the realignment method, if needed. Hamming distance does not require a path to a tool.
- 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.
A modifed input
data.frame containing the best allele call from
among the sequences listed in
genotype_db in the
In order to save time, initial gene assignments are preserved and
the allele calls are chosen from among those provided in
based on a simple alignment to the sample sequence.
# Extract the database sequences that correspond to the genotype genotype_db <- genotypeFasta(SampleGenotype, GermlineIGHV, novel=SampleNovel) # Use the personlized genotype to determine corrected allele assignments output_db <- reassignAlleles(SampleDb, genotype_db)