VLF (version 1.1)

aa.specimen.frequencies: Specimen Nucleotide Frequencies

Description

Converts a matrix of amino acid sequences into a matrix of amino acid frequencies.

Usage

aa.specimen.frequencies(freq, seq.matrix, spec.names, seqlength)

Value

A matrix containing the frequencies of each amino acid in the sequence.

Arguments

freq

Frequency matrix for amino acids.

seq.matrix

Matrix of specimen amino acid sequences.

spec.names

A vector of the species names for each specimen in aminoAcids in the ordfer they appear in the matrix.

seqlength

Length of amino acid sequences.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument freq can be calculated using the function aa.frequency.matrix.function.

Examples

if (FALSE) data(birds_aminoAcids)
birds_aminoAcid_speciesNames <- birds_aminoAcids[,2]
aminoAcids_specimenNumber <- nrow(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids,216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count,216)
bird_aminoAcid_frequencies <- aa.specimen.frequencies(aminoAcid_frequency.Matrix, birds_aminoAcids,
    birds_aminoAcid_speciesNames, 216)