find.singles: Single and Shared VLF Find

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

Single and Shared VLF Find

Description

Calculates the number of singleton and shared VLFs for each position of the nucleotide, by first seeing if there is only one specimen for a species, and then calling on the compare() function to calculate the number of singleton and shared VLFs for those species with multiple specimen.

Usage

find.singles(species, seqlength)

Arguments

species	A list of sequences separated byh species name. Each entry in the list contains a matrix of sequences from the same species.
seqlength	Length of the nucleotide sequence.

Details

The argument species can be calculated using the separate function.

Value

A matrix containing the number of singleton and shared ntVLFs in each position of the barcode.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: #Nucleotide VLF analysis
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)
Bird_specimen_VLFcount <- VLF.count.spec(birdSpec.freq, 0.001, 648)
bird_VLFconvert <- VLF.convert.matrix(birds, birdSpec.freq, 0.001, 648)
bird_VLFnuc <- VLF.nucleotides(bird_VLFconvert, birds, 648)
bird_VLFreduced <- VLF.reduced(bird_VLFnuc, Bird_specimen_VLFcount, 648)
bird_species <- separate(bird_VLFreduced)
birds_singleAndShared <- find.singles(bird_species, 648)
## End(Not run)

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