VLF (version 1.1)

compare: Compare VLFs within Species

Description

Compares VLFs between specimen of the same species.

Usage

compare(x, seqlength)

Value

A matrix containing two vectors, one with singleton VLF counts for each position of the sequence, and one with shared VLF counts for each position of the sequence.

Arguments

x

A list of sequences separated by species name. Each entry in the list contains a matrix of sequences from the same species.

seqlength

Length of the sequences.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

List of sequences by species names, x, can be created using the separate 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)
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)

#The compare function is called on from within the find.singles function
birds_singleAndShared <- find.singles(bird_species, 648)