CodonUsage_DNA {ftrCOOL}

Codon Usage in DNA (CodonUsage_DNA)

Description

This function calculates the codon usage for each sequence.

Usage

CodonUsage_DNA(seqs, ORF = FALSE, reverseORF = TRUE, label = c())

Arguments

seqs

is a FASTA file containing nucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a nucleotide sequence.

ORF

(Open Reading Frame) is a logical parameter. If it is set to true, ORF region of each sequence is considered instead of the original sequence (i.e., 3-frame).

reverseORF

is a logical parameter. It is enabled only if ORF is true. If reverseORF is true, ORF region will be searched in the sequence and also in the reverse complement of the sequence (i.e., 6-frame).

label

is an optional parameter. It is a vector whose length is equivalent to the number of sequences. It shows the class of each entry (i.e., sequence).

Value

A feature matrix such that the number of columns is 4^3 and the number of rows is equal to the number of sequences.

Examples

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
mat<-CodonUsage_DNA(fileLNC,ORF=TRUE,reverseORF=FALSE)