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)
Arguments¶
- genotype
data.frameof 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.framecontaining 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¶
# Find the sequences that correspond to the genotype
genotype_db <- genotypeFasta(SampleGenotype, SampleGermlineIGHV, SampleNovel)