getClosestComplete,IpdDb-method {ipdDb}R Documentation

Get closest full-length sequence

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])


[Package ipdDb version 1.10.0 Index]