aa.specimen.frequencies: Specimen Nucleotide Frequencies

In VLF: Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records

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)

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.

Details

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

Value

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

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
## End(Not run)

VLF documentation built on April 12, 2025, 1:22 a.m.