aa.conservation_two: First and Second Modal Amino Acid Conservation

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

First and Second Modal Amino Acid Conservation

Description

Calculates the conservation of the amino acids that occur first and second most often in a matrix of sequences

Usage

aa.conservation_two(modal1, modal2, p, seqlength)

Arguments

modal1	A vector of the frequencies for the amino acids in the first modal sequence.
modal2	A vector of the frequencies for the amino acids in the second modal sequence
p	A conservation value for the amino acid frequencies to be compared to.
seqlength	The length of the amino acid sequence.

Details

The argument modal1 can be calculated using the aa.MODE.freq function, and the argument modal2 can be calculated using he aa.MODE.second.freq function.

Value

A vector that contains how many amino acids from the first and second modal sequences 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_secondModalFreq <- aa.MODE.second.freq(aminoAcid_frequency.Matrix, 216)
aminoAcid_secondConservation_99.9 <- aa.conservation_two(aminoAcid_firstModalFreq, 
    aminoAcid_secondModalFreq, 0.999, 216)
## End(Not run)

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