separate: Separate Specimen by Species Names

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

Separate Specimen by Species Names

Description

Separates specimen into lists by species names.

Usage

separate(x)

Arguments

x	A matrix of sequences, usually reduced sequences containing only VLFs, where the second position of the matrix contains the species name for the specimen.

Details

If the argument x needs to be a reduced matrix, it can be calculated using the function VLF.reduced.

Value

A list containing a matrix of sequences for each species.

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_position_VLFcount <- VLF.count.pos(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)
## End(Not run)

VLF documentation built on Aug. 18, 2022, 5:06 p.m.