parseHLADbAlignment: Parse 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

Parse HLA Database alignment files that are present in a directory, as specified by input, an generate a class object that can be used in further analysis. The function only parse one type of aligment file at the time. There is 3 types of alignment files that can be parsed: CDS sequence, genomic and protein.

Beware that the names of the alignment files should not be changed as the name is used to identify the gene that is currently parsed.

Usage

parseHLADbAlignment(hlaDbPath, seqType = c("prot", "nuc", "gen"))

Arguments

hlaDbPath	A character string, the path to the directory of the alignment files from http://hla.alleles.org/alleles/text_index.html. The directory must exist and contain at least one HLA alignment file.
seqType	A character string, the sequence type of the file to parse. The choices are: "nuc" for CDS sequence, "gen" for genomic, and "prot" for protein. Default: "prot".

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 <- parseHLADbAlignment(hlaDbPath=directory, seqType="prot")

## Show reference sequences
HLAInfo$refSeq

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