aa.conservation_first: First Modal Amino Acid Conservation

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

First Modal Amino Acid Conservation

Description

Calculates the conservation of the first amino acids that occur most often in a matrix of amino acid sequences.

Usage

aa.conservation_first(modal, p, seqlength)

Arguments

modal	A vector of the frequencies for the amino acids in the first modal sequence.
p	A conservation value for the amino acid frequencies to be compared to
seqlength	Length of the amino acid sequence

Details

The item modal can be calculated using the aa.MODE.freq function.

Value

A vector that contains how many amino acids from the first modal sequence are conserved at the specified conservation level.

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_Modal <- aa.MODE(aminoAcid_frequency.Matrix, 216)
aminoAcid_firstModalFreq <- aa.MODE.freq(aminoAcid_frequency.Matrix, 216)
aminoAcid_firstConservation_100 <- aa.conservation_first(aminoAcid_firstModalFreq, 1, 216)
## End(Not run)

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