conservation_first: First Modal Conserved

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

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)

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.

Details

The argument modal can be calculated using the MODE.freq function.

Value

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

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)
First_conserved_100 <- conservation_first(Bird_first.modal.frequencies, 1, 648)
First_conserved_99.9 <- conservation_first(Bird_first.modal.frequencies, 0.999, 648)
## End(Not run)

VLF documentation built on April 12, 2025, 1:22 a.m.