getClosestComplete-IpdDb-method: Get closest full-length sequence

In ipdDb: IPD IMGT/HLA and IPD KIR database for Homo sapiens

Description

Get the sequence of the closest allele which for which a full-length sequence is available.

Usage

getClosestComplete(x, allele, locus = NULL)

Arguments

x	The database connection; an IpdDb object.
allele	A single allele as a string.
locus	optional parameter used if the allele identifier is not found.

Value

A Biostrings:DNAStringSet object with the sequence of the closest full-length allele.

Examples

## Load the database 
hla <- loadHlaData()
## Get the loci
loci <- getLoci(hla)
## Get alleles of a locus
alleles <- getAlleles(hla, loci[1])
alleleOfInterest <- alleles[1]
## Get the closest complete sequence
seqs <- getClosestComplete(hla, alleleOfInterest, loci[1])

ipdDb documentation built on Nov. 8, 2020, 6:07 p.m.