MODE: Modal Sequence

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

Modal Sequence

Description

Calculates the nucleotide sequence that occurs most often in a matrix of sequences.

Usage

MODE(freq, seqlength)

Arguments

freq	Frequenct matrix for nucleotides.
seqlength	Length of nucleotide sequence.

Details

The argument freq can be calculated using the function ffrequency.matrix.function.

Value

A vector containing the first modal 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)
nucleotide.modalSequence <- MODE(frequency.matrix, 648)
## End(Not run)

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