VLF (version 1.1)

MODE.second.freq: 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)

Value

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

Arguments

freq

Frequency matrix for nucleotides.

seqlength

Length of nucleotide sequences.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

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

Examples

if (FALSE) 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)