View source: R/VLF.nucleotides.R
VLF.nucleotides | R Documentation |
Converts a matrix of nucleotide frequencies for each specimen into a matrix of nucleotides for each specimen.
VLF.nucleotides(convert.matrix, seq.matrix, seqlength)
convert.matrix |
A matrix consisting of only very low frequency cariant frequencies for each specimen, and NAs in all other positions of the sequence. |
seq.matrix |
A matrix of DNA sequences. |
seqlength |
The length of the sequences. |
The argument convert.matrix can be calculated using the function VLF.convert.matrix.
A matrix containing only ntVLFs in each position of the sequences, and NAs in all other positions.
## Not run: data(birds) species.names <- birds[,2] specimen.Number <- nrow(birds) rownames(birds) <- species.names Nuc.count <- count.function(birds, specimen.Number, 648) frequency.matrix <- ffrequency.matrix.function(Nuc.count, 648) birdSpec.freq <- specimen.frequencies(frequency.matrix, birds, specimen.Number, species.names, 648) Bird_specimen_VLFcount <- VLF.count.spec(birdSpec.freq, 0.001, 648) bird_VLFconvert <- VLF.convert.matrix(birds, birdSpec.freq, 0.001, 648) bird_VLFnuc <- VLF.nucleotides(bird_VLFconvert, birds, 648) ## End(Not run)
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