VLF.aminoAcids {VLF} | R Documentation |
Amino Acid VLFs
Description
Converts a matrix of amino acid frequencies into a matrix of amino acids.
Usage
VLF.aminoAcids(convert.matrix, seq.matrix, seqlength)
Arguments
convert.matrix |
A matrix consisting of only aaVLF frequencies for each specimen, and NAs in every other position of the sequence. |
seq.matrix |
A matrix of amino acid sequences. |
seqlength |
The length of the amino acid sequence. |
Details
The argument convert.matrix can be calculated using the function aa.VLF.convert.matrix
Value
A matrix containing only aaVLFs and NAs in every other position of the sequence.
Author(s)
Taryn B. T. Athey and Paul D. McNicholas
Examples
## Not run: data(birds_aminoAcids)
birds_aminoAcid_speciesNames <- birds_aminoAcids[,2]
aminoAcids_specimenNumber <- nrow(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
bird_aminoAcid_frequencies <- aa.specimen.frequencies(aminoAcid_frequency.Matrix, birds_aminoAcids,
birds_aminoAcid_speciesNames, 216)
aminoAcid_Modal <- aa.MODE(aminoAcid_frequency.Matrix, 216)
birds_aminoAcid_specimenVLFcount <- aa.VLF.count.spec(bird_aminoAcid_frequencies, 0.001, 216)
birds_aaVLFconvert <- aa.VLF.convert.matrix(birds_aminoAcids, bird_aminoAcid_frequencies, 0.001,
216)
birds_aminoAcidVLFs <- VLF.aminoAcids(birds_aaVLFconvert, birds_aminoAcids, 216)
## End(Not run)
[Package VLF version 1.1 Index]