Description Usage Arguments Value Examples
View source: R/CodonUsage_RNA.R
This function calculates the codon usage for each sequence.
1 | CodonUsage_RNA(seqs, ORF = FALSE, reverseORF = TRUE, label = c())
|
seqs |
is a FASTA file containing ribonucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a ribonucleotide 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). |
A feature matrix such that the number of columns is 4^3 and the number of rows is equal to the number of sequences.
1 2 | fileLNC<-system.file("extdata/Carica_papaya101RNA.txt",package="ftrCOOL")
mat<-CodonUsage_RNA(seqs=fileLNC,ORF=TRUE,reverseORF=FALSE)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.