readHLADataset: Extract HLA typing information for all samples present in a...

In NCBI-Hackathons/HLAClustRView: HLA typing clustering and visualization based on specific similarity metrics

Description

Parses a text file containing HLA allele typing for one or multiple samples and transforms it into an object. Beware that samples with at least one missing HLA type for the allele group are going to be removed.

Usage

readHLADataset(hlaFilePath)

Arguments

hlaFilePath

a character string, the filepath to a text file containing the information about the samples typing. The name must correspond to an existing text file. The text file must have a header.

Value

a list of class HLADataset containing the following elements:

• data a tibble object containing the HLA typing information for all samples. The columns are:

  • SampleName a character string that represent the name of the sample.

  • AllelName a character string that represent the name of the allele (1 or 2).

  • GeneName a character string that represent the name of the HLA gene.

  • AlleleGroup a character string that represent the section identifying the subtype group.

  • Protein a character string that represent the section identifying the nucleotide substitutions group.

  • SynSubst a character string that represent the section identifying the synonymous nucleotide substitutions group.

  • NonCoding a character string that represent the section identifying the non-coding polymorphisms group.

  • Suffix a character string that represent the suffix of the HLA typing or NA.

Author(s)

Adewunmi Adelaja

Examples

## Get path where some HLA database files are stored
directory <- system.file("extdata", package = "HLAClustRView")
fileName <- paste0(directory, "/Samples_HLA_typing.txt")

## Parse file to extract HLA typing for all samples
ex <- readHLADataset(hlaFilePath=fileName)

## Show the output HLADataset object
print(ex)

NCBI-Hackathons/HLAClustRView documentation built on Nov. 22, 2019, 6:11 a.m.