PALM {SSHAARP}

Population Allele Locating Mapmaker

Description

Produces a frequency heatmap for a specified amino-acid motif, based on the allele frequency data in the Solberg dataset.

Usage

PALM(
  motif,
  filename = SSHAARP::solberg_dataset,
  direct = getwd(),
  color = TRUE,
  filterMigrant = TRUE
)

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.

direct

The directory into which the map produced is written. The default directory is the user's working directory.

color

A logical parameter that identifies if the heat maps should be made in color (TRUE) or gray scale (FALSE). The default option is TRUE.

filterMigrant

A logical parameter that determines if admixed populations (OTH) and migrant populations (i.e. any complexities with the 'mig') should be excluded from the dataset. The default option is TRUE.

Value

The specified motif and the directory into which the heatmap was written are returned in an invisible character vector. If the user enters a motif that is not found in the Solberg dataset, or that does not exist, a warning message is returned. If an incorrectly formatted motif is entered, or the user does not have the GMT software installed on their operating system, a vector with a warning message is returned. The produced heatmap is written to the user's specified directory (default is user's working directory) as a .jpg file, where the filename is "'motif'.jpg".

Note

The produced frequency heatmap is generated by using the Generic Mapping Tools (GMT) R Package, which is an interface between R and the GMT Map-Making software.

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'.

While the map legend identifies the highest frequency value, values in this range may not be represented on the map due to frequency averaging over neighboring populations.

References

Solberg et.al. (2008) <doi: 10.1016/j.humimm.2008.05.001>

Examples

#example to produce a color frequency heat map where migrant populations are filtered out
PALM("DRB1*26F~28E~30Y",filename = solberg_dataset[85:100,], filterMigrant=TRUE)
#example to produce a greyscale heat map where migrant populations are not filtered out
PALM("DRB1*26F~28E~30Y", filename = solberg_dataset[85:100,], color=FALSE, filterMigrant=FALSE)