VLF (version 1.1)

aa.VLF.count.pos: VLF position count

Description

Calculates the number of very low frequency variants in each position in a matrix of sequences

Usage

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

Value

A vector containing the amino acid VLF count for each position of the sequence.

Arguments

freq

A matrix of frequencies for each speicmen.

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.

Author

Taryn B. T. Athey and Paul D. McNicholas

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)
birds_aminoAcid_positionVLFcount <- aa.VLF.count.pos(bird_aminoAcid_frequencies, 0.001, 216)