parseAlignment: Pre-process HLA Database alignment file

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

Description

Extract information from one HLA alignment file.

Usage

parseAlignment(fileName)

Arguments

fileName

A character string, the name of the alignment file from http://hla.alleles.org/alleles/text_index.html.

Details

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

Value

A list containing:

• refSeq A character string that represent the reference sequence.

• posInit A integer that represent the starting position of the gene.

• HLAalignment A data.table containing the information for all types associated to the HLA gene.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Set the name of the aligment file to be processed
fileInfo <- paste0(system.file("extdata", package = "HLAClustRView"),
    "/DRA_prot.txt")

## Parse aligment file
HLAClustRView:::parseAlignment(fileName=fileInfo)

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