dataSubset: Solberg dataset manipulation

In SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

Description

Returns a modified version of the Solberg 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(motif, filename = SSHAARP::solberg_dataset)

Arguments

motif	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.
filename	The filename of the local copy of the Solberg dataset - the defaulted filename is the solberg_dataset in the SSHAARP package.

Value

A data frame containing a reformatted version of the Solberg 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. If a motif has formatting errors, a warning message is returned.

Note

For internal SSHAARP use only.

The Solberg dataset is the tab-delimited ‘1-locus-alleles.dat’ text file in the results.zip archive at http://pypop.org/popdata/.

The Solberg dataset is also prepackaged into SSHAARP as 'solberg_dataset'.

SSHAARP documentation built on Sept. 17, 2021, 9:07 a.m.