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_alignment",
method = "hamming",
path = NA,
keep_gene = c("gene", "family", "repertoire")
)
Arguments¶
- data
data.frame
containing V allele calls from a single subject and the sample IMGT-gapped V(D)J sequences underseq
.- genotype_db
- 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 isv_call
. - seq
- name of the column in
data
with the aligned, IMGT-numbered, V(D)J nucleotide sequence. Default is SEQUENCE_IMGT - method
- method to use 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
- 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(AIRRDb, genotype_db, v_call="v_call",
seq="sequence_alignment")