VLF (version 1.1)

aa.conservation_first: 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)

Value

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

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

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

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

Examples

if (FALSE) 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)