Compares VLFs between specimen of the same species.
A list of sequences separated by species name. Each entry in the list contains a matrix of sequences from the same species.
Length of the sequences.
List of sequences by species names, x, can be created using the separate function
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.
Taryn B. T. Athey and Paul D. McNicholas
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## 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) 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) ## End(Not run)
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