MODE.second.freq: Second Modal Frequency

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

Second Modal Frequency

Description

Calculates the frequencies of the nucleotides that occur second most often in a matrix of sequences.

Usage

MODE.second.freq(freq, seqlength)

Arguments

freq	Frequency matrix for nucleotides.
seqlength	Length of nucleotide sequences.

Details

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

Value

A vector containing the frequencies of the nucleotide sequence that occurs second most often.

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)
Bird_second.modal.frequencies <- MODE.second.freq(frequency.matrix, 648)
## End(Not run)

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