aa.conservation_two {VLF} | R Documentation |
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)
[Package VLF version 1.1 Index]