reassignAlleles: Correct allele calls based on a personalized genotype

In tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data

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"),
  trim_seq = FALSE,
  overwrite = FALSE,
  ignored_regex = "[\\.N-]",
  treat_multigene_as_uncalled = FALSE,
  top_k = NULL,
  top_by = c("alphabetical", "mutation_count"),
  strip_d = TRUE,
  reassign_uncalled = TRUE
)

Arguments

data	data.frame containing V allele calls from a single subject and the sample IMGT-gapped V(D)J sequences under seq.
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 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	method to use when realigning sequences to the genotype_db sequences. Currently, only "hamming" (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.
trim_seq	if TRUE, trim sample and germline sequences to the segment boundaries before calculating Hamming distance. Boundaries are determined from the segment prefix of v_call, such as v_*, d_*, or j_* columns.
overwrite	if TRUE, replace v_call with reassigned calls instead of writing a *_call_genotyped column.
ignored_regex	regular expression indicating characters to ignore when comparing sequences. May also be TRUE to ignore nothing (every position counts), as used for D and J segments.
treat_multigene_as_uncalled	if TRUE, sequences whose call spans more than one gene are treated as uncalled and realigned against the whole genotype rather than kept at their first gene. Only applies when keep_gene is "gene" or "repertoire".
top_k	maximum number of equally-best alleles to report per sequence. NULL (default) keeps all ties.
top_by	how to break ties when more than top_k alleles are equally close. "alphabetical" keeps the first top_k by name; "mutation_count" keeps all ties.
strip_d	if TRUE (default) remove the "D" from the end of gene annotations (denoting a duplicate gene in the locus) when grouping the genotype_db alleles by gene. If FALSE, the "D" is kept, so the genotype grouping and the sequence calls are matched consistently (use together with genotypeFasta(strip_d=FALSE)).
reassign_uncalled	if TRUE (default), sequences whose call is empty or NA are also realigned against the whole genotype. If FALSE, they are left unassigned.

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.

Value

A modified input data.frame containing the best allele call from among the sequences listed in genotype_db in the *_call_genotyped column, or in v_call when overwrite=TRUE.

Examples

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

# Use the personalized genotype to determine corrected allele assignments
output_db <- reassignAlleles(AIRRDb, genotype_db, v_call="v_call",
                             seq="sequence_alignment")

tigger documentation built on Oct. 7, 2026, 1:07 a.m.