Converts a matrix of amino acid frequencies into a matrix of amino acids.
VLF.aminoAcids(convert.matrix, seq.matrix, seqlength)
A matrix containing only aaVLFs and NAs in every other position of the sequence.
A matrix consisting of only aaVLF frequencies for each specimen, and NAs in every other position of the sequence.
A matrix of amino acid sequences.
The length of the amino acid sequence.
Taryn B. T. Athey and Paul D. McNicholas
The argument convert.matrix can be calculated using the function aa.VLF.convert.matrix
if (FALSE) 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)
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