conservation_two: First and Second Modal Conserved

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

First and Second Modal Conserved

Description

Calculates the conservation of the nucleotides that occur first and second most often in a matrix of sequences.

Usage

conservation_two(modal1, modal2, p, seqlength)

Arguments

modal1	A vector of the frequencies for the nucleotides in the first modal sequence.
modal2	A vector of the frequencies for the nucleotides that occur second most often.
p	A conservation value for the nucleotide frequencies to be compared to.
seqlength	The nucleotide sequence length.

Details

The argument modal1 can be calculated using the function MODE.freq. The argument modal2 can be calculated using the function MODE.second.freq.

Value

A vector that contains how many nucleotides from the first and second modal sequences 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)
Bird_second.modal.frequencies <- MODE.second.freq(frequency.matrix, 648)
FirstAndSecond_conserved_99.9 <- conservation_two(Bird_first.modal.frequencies, 
    Bird_second.modal.frequencies, 0.999, 648)
## End(Not run)

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