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_df = NA)

Arguments

genotype
a table of alleles denoting a genotype, as returned by inferGenotype
germline_db
a vector of named nucleotide germline sequences matching the alleles detailed in genotype
novel_df
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

Examples

# Load example data
data(germline_ighv)
data(novel_df)
data(genotype)

# Find the sequences that correspond to the genotype
genotype_seqs = genotypeFasta(genotype, germline_ighv, novel_df)

See also

inferGenotype