genotypeFasta {tigger}

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)

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 alleeles of the type returned by findNovelAlleles.

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)