aa.VLF.count.pos: VLF position count

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

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)

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.

Value

A vector containing the amino acid VLF count for each position of 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)
birds_aminoAcid_positionVLFcount <- aa.VLF.count.pos(bird_aminoAcid_frequencies, 0.001, 216)
## End(Not run)

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