aa.conservation_first {VLF}

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)