Description Usage Arguments Value Note References Examples
Produces a frequency heatmap for a specified amino-acid motif, based on the allele frequency data in the Solberg dataset.
1 2 3 4 5 6 7 | PALM(
motif,
filename = SSHAARP::solberg_dataset,
direct = getwd(),
color = TRUE,
filterMigrant = TRUE
)
|
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. |
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".
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.
Solberg et.al. (2008) <doi: 10.1016/j.humimm.2008.05.001>
1 2 3 4 | #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)
|
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