aa.VLF.count.spec {VLF}

VLF Specimen Count

Description

Calculates the number of very low frequency variants for each specimen in a matrix of sequences.

Usage

aa.VLF.count.spec(freq, p, seqlength)

Arguments

freq

A matrix of amino acid frequencies for each specimen.

p

A very low frequency variant cut-off frequency. Any frequency in the freq matrix below this value is considered to be a very low frequency variant.

seqlength

The length of the amino acid sequences.

Value

A vector containing the aaVLF count for every specimen.

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)
birds_aminoAcid_specimenVLFcount <- aa.VLF.count.spec(bird_aminoAcid_frequencies, 0.001, 216)
## End(Not run)