compare: Compare VLFs within Species

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

Compare VLFs within Species

Description

Compares VLFs between specimen of the same species.

Usage

compare(x, seqlength)

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.

Details

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

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.

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)
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)

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