VLF (version 1.1)

find.singles: 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)

Value

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

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.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument species can be calculated using the separate function.

Examples

if (FALSE) #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)