VLF.convert.matrix: VLF Matrix Convert

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

VLF Matrix Convert

Description

Converts a matrix of nucleotide frequencies for each specimen into a matrix consisting entirely of very low frequency variant (VLF) frequencies and NAs in each other position.

Usage

VLF.convert.matrix(seq.matrix, freq, p, seqlength)

Arguments

seq.matrix	A matrix of aligned DNA barcode sequences.
freq	A matrix of nucleotide frequencies for each specimen.
p	A very low frequency variant designation cut off frequency. Any frequency in the freq matrix below this value is considered to be a very low frequency variant.
seqlength	Length of nucleotide sequence.

Details

The argument freq can be calculated using the function specimen.frequencies.

Value

A matrix of VLF nucleotide frequencies, containing only those nucleotide frequencies that occur less than the designation p value, and NAs in each other position of the matrix.

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)
aminoAcid_Modal <- aa.MODE(aminoAcid_frequency.Matrix, 216)
birds_aminoAcid_specimenVLFcount <- aa.VLF.count.spec(bird_aminoAcid_frequencies, 0.001, 216)
birds_aaVLFconvert <- aa.VLF.convert.matrix(birds_aminoAcids, bird_aminoAcid_frequencies,0.001,216)
## End(Not run)

VLF documentation built on Aug. 18, 2022, 5:06 p.m.