VariantFiltering (version 1.8.6)

readAAradicalChangeMatrix: Read matrix of amino acid radical changes

Description

Function to read and parse a tab-separated file of amino acid properties into a matrix of logical values indicating whether the change of one amino acid by another can be considered radical or conservative according to the chemical properties specified in the input file.

Usage

readAAradicalChangeMatrix(file)

Arguments

file

A file containing a classification of amino acids with respect to one or more chemical properties. Its particular format should match the one from the file called AA_chemical_properties_HanadaGojoboriLi2006.tsv found in the extdata folder of this package. This file is based on Table 1 from Hanada et al. (2006).

Value

An squared symmetric matrix with as many rows and columns as amino acids and whose cells contain logical values. These values are set to TRUE whenever the amino acid change implied by row and column is considered radical and FALSE when considered conservative. Amino acid changes within a chemical property are defined as conservative and radical otherwise.

Details

The input file should contain one or more columns each of them forming a logical mask specifing sets of amino acids sharing some chemical property.

References

Hanada, K., Gojobori, T. and Li, W. Radical amino acid change versus positive selection in the evolution of viral envelope proteins. Gene, 385:83-88, 2006.

See Also

VariantFilteringParam

Examples

aamat <- readAAradicalChangeMatrix(file.path(system.file("extdata", package="VariantFiltering"),
                                   "AA_chemical_properties_HanadaGojoboriLi2006.tsv"))
aamat[1:5, 1:5]