genotypeFasta - 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.

Examples¶

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

See also¶

inferGenotype