loadHLADb: load HLA Database alignment files for a specific alignment...

In NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq: HLA typing clustering and visualization based on specific similarity metrics

Description

load HLA Database parse by parseHLADbAlignment

Usage

loadHLADb(hlaDbFile)

Arguments

hlaDbFile

A character string, the path to the rds file from parseHLADbAlignment. #'

Details

See http://hla.alleles.org/alleles/text_index.html

Value

An object of class HLAdb with 3 entries. The entries are:

• refSeq A list of character string that represent reference sequences; one sequence per HLA gene.

• posInit A list of integer; one starting position per HLA gene.

• HLAAlignment A data.table containing the information for each allele of each HLA gene.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Get path where some HLA database files are stored
##directory <- system.file("extdata", package = "HLAClustRView")

## Parse HLA database files of protein type
##HLAInfo <- loadHLADb(hlaDbFile="")

## Show reference sequences
##HLAInfo$refSeq

NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq documentation built on Nov. 23, 2019, 1:57 a.m.