dataSubset: Dataset manipulation for motifs and alleles
In SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

dataSubset

R Documentation

Dataset manipulation for motifs and alleles

Description

Returns a modified version of the user selected dataset that includes a column of locus*allele names, is sorted by by population name, and is reduced to the specified locus. Cardinal coordinates are converted to their Cartesian equivalents (i.e. 50S is converted to -50).

Usage

dataSubset(variant, filename)

Arguments

`variant`	An allele or an amino acid motif in the following format: Locus*##$~##$~##$, where ## identifies a peptide position, and $ identifies an amino acid residue. Motifs can include any number of amino acids. Haplotypes must contain alleles that follow the aforementioned format, and may be delimited by "~".
`filename`	The full file path of the user specified dataset if the user wishes to use their own file, or the pre-bundled Solberg dataset. User provided datasets must be a .dat, .txt, or.csv file, and must conform to the structure and format of the Solberg dataset.

Value

A data frame containing a reformatted version of the user selected dataset, with rows ordered by population name, Cartesian coordinates in the latit and longit columns, and limited to populations with data for the specified locus. Otherwise, a vector containing FALSE and an error message is returned.