VLF (version 1.1)

aa.conservation_two: 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)

Value

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

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.

Author

Taryn B. T. Athey and Paul D. McNicholas

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.

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_secondModalFreq <- aa.MODE.second.freq(aminoAcid_frequency.Matrix, 216)
aminoAcid_secondConservation_99.9 <- aa.conservation_two(aminoAcid_firstModalFreq, 
    aminoAcid_secondModalFreq, 0.999, 216)