Description Usage Arguments Value Author(s) References See Also Examples
The function reads aligned sequences in a fasta file and estimates the codon usage bias for each sequence. Several methods exist to estimate CUB; so far, only the "Effective Number of Codons" (ENC) calculation is available.
1 |
file |
FASTA file in which aligned sequences are stored. |
sequence |
Alternatively, the result of seqinr::read.fasta. |
method |
The method used to compute CUB. "ENC": Effective Number of Codons, as described in Wright (1990). |
A named vector of CUB scores. Names correspond to sequence names in the dataset.
Aurelie Hua-Van and Arnaud Le Rouzic.
Wright, F. (1990). The 'effective number of codons' used in a gene. Gene, 87(1), 23-29.
1 2 | seq.file <- system.file("extdata/Genes", "Amd.fas", package="vhica")
CUB(seq.file)
|
dgri dvir dmoj dwil dpse dper dana dbip
47.87244 40.18310 51.40403 48.91050 49.25746 48.89993 44.63742 42.75869
dkik deug dfic dmel dsim dsec dere dyak
44.80419 55.86458 46.33597 48.18881 43.45357 44.85876 44.13209 45.38671
dbia dtak dele drho
38.20318 42.14270 40.44045 42.95457
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