count.function: Nucleotide Count

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

Nucleotide Count

Description

Counts the number of each dNTP in each position of an aligned barcode matrix.

Usage

count.function(nucleotides, spec.no, seqlength)

Arguments

nucleotides	A matrix of aligned DNA barcode sequences. DNA sequences should start at the third column of the matrix, while the first column contains a unique specimen identifier and the second column contains the species name.
spec.no	The number of specimen/sequences in the nucldeotide matrix.
seqlength	The length of the nucleotide sequences.

Value

A matrix containing the number of each nucleotide in each position of the sequence. Each row is a different dNTP count, while the columns represent the sequence position.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds)
Nuc.count <- count.function(birds, specimen.Number, 648)
## End(Not run)

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