readHlaAlignments {midasHLA} | R Documentation

## Read HLA allele alignments

### Description

`readHlaAlignments` read HLA allele alignments from file.

### Usage

    readHlaAlignments(file, gene = NULL, trim = FALSE, unkchar = "")

### Arguments

`file` | Path to input file.
`gene` | Character vector of length one specifying the name of a gene for which alignment is required. See details for further explanations.
`trim` | Logical indicating if alignment should be trimmed to start codon of the mature protein.
`unkchar` | Character to be used to represent positions with unknown sequence.

### Details

HLA allele alignment file should follow EBI database format, for details see ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/alignments/README.md.

All protein alignment files from the EBI database are shipped with the package. They can be easily accessed using `gene` parameter. If `gene` is set to `NULL`, `file` parameter is used instead and alignment is read from the provided file. In EBI database alignments for DRB1, DRB3, DRB4 and DRB5 genes are provided as a single file, here they are separated.

Additionally, for the alleles without sequence defined in the original alignment files we have infered thier sequence based on known higher resolution alleles.

### Value

Matrix containing HLA allele alignments.

Rownames correspond to allele numbers and columns to positions in the alignment. Sequences following the termination codon are marked as empty character (`""`). Unknown sequences are marked with a character of choice, by default `""`. Stop codons are represented by a hash (X). Insertion and deletions are marked with period (.).

### Examples

    hla_alignments <- readHlaAlignments(gene = "A")

[Package midasHLA version 1.2.0 Index]