genotypeFasta: Return the nucleotide sequences of a genotype

In tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data

Return the nucleotide sequences of a genotype

Description

genotypeFasta converts a genotype table into a vector of nucleotide sequences.

Usage

genotypeFasta(
  genotype,
  germline_db,
  novel = NA,
  include_unseen = FALSE,
  strip_d = TRUE
)

Arguments

genotype	data.frame of alleles denoting a genotype, as returned by inferGenotype.
germline_db	vector of named nucleotide germline sequences matching the alleles detailed in genotype.
novel	an optional data.frame containing putative novel alleles of the type returned by findNovelAlleles.
include_unseen	if TRUE, include germline database alleles for genes that are not present in genotype. For genes present in genotype, include only the genotyped alleles.
strip_d	if TRUE (default) remove the "D" from the end of gene annotations (denoting a duplicate gene in the locus) when matching genotype alleles to germline_db. If FALSE, alleles are matched exactly.

Value

A named vector of strings containing the germline nucleotide sequences of the alleles in the provided genotype.

See Also

inferGenotype

Examples

# Find the sequences that correspond to the genotype
genotype_db <- genotypeFasta(SampleGenotype, SampleGermlineIGHV, SampleNovel)

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