MODE.freq: Modal Frequencies

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

Modal Frequencies

Description

Returns the frequencies of the nucleotides in each position of nucleotide sequence that occurs most often.

Usage

MODE.freq(freq, seqlength)

Arguments

freq	Frequency matrix for nucleotides.
seqlength	Length of the nucleotide sequence.

Details

The argument freq can be calculated using the function ffrequency.matrix.function.

Value

A vector of frequencies for the first modal sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds)
species.names <- birds[,2]
specimen.Number <- nrow(birds)
rownames(birds) <- species.names
Nuc.count <- count.function(birds, specimen.Number, 648)
frequency.matrix <- ffrequency.matrix.function(Nuc.count, 648)
birdSpec.freq <- specimen.frequencies(frequency.matrix, birds, specimen.Number, species.names, 648)
nucleotide.modalSequence <- MODE(frequency.matrix, 648)
Bird_first.modal.frequencies <- MODE.freq(frequency.matrix, 648)
## End(Not run)

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