aa.MODE.second.freq: Amino Acid Second Modal Frequency

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

Amino Acid Second Modal Frequency

Description

Returns the frequencies of the amino acids that occur second most often in each position of a matrix of amino acid sequences.

Usage

aa.MODE.second.freq(freq.matrix, seqlength)

Arguments

freq.matrix	Frequency matrix for amino acids.
seqlength	Length of amino acid sequences.

Details

The argument freq.matrix can be calculated using the function aa.frequency.matrix.function

Value

A vector containing the frequencies of the second modal amino acid sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
aminoAcid_secondModalFreq <- aa.MODE.second.freq(aminoAcid_frequency.Matrix, 216)
## End(Not run)

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