VLF (version 1.1)

conservation_first: First Modal Conserved

Description

Calculates the conservation of the nucleotides that occur most often in a matrix of sequences/

Usage

conservation_first(modal, p, seqlength)

Value

A vector that contains how many nucleotides from the first modal sequence are conserved at the specified conservation level for each codon position.

Arguments

modal

A vector of the frequencies of the nucleotides in the first modal sequences.

p

A conservation value for the nucleotide frequencies to be compared to.

seqlength

The length of the nucleotide sequence.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument modal can be calculated using the MODE.freq 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)
First_conserved_100 <- conservation_first(Bird_first.modal.frequencies, 1, 648)
First_conserved_99.9 <- conservation_first(Bird_first.modal.frequencies, 0.999, 648)