ENc.values: Effective Number of Codons (ENc).
In vhcub: Virus-Host Codon Usage Co-Adaptation Analysis

Description Usage Arguments Details Value Author(s) Examples

Measure the Effective Number of Codons (ENc) of DNA sequence. Using its modified version (Novembre, 2002).

1	ENc.values(df.fasta,genetic.code = "1",threshold=0)

`df.fasta`	a data frame with seq_name and its DNA sequence.
`genetic.code`	a single string that uniquely identifies a genetic code to use.
`threshold`	optional numeric, specifying sequence length, in codons, used for filtering.

For more information about ENc Novembre, 2002.

A data.frame containing the computed ENc values for each DNA sequences within df.fasta.

Ali Mostafa Anwar ali.mo.anwar@std.agr.cu.edu.eg and Mohmed Soudy MohmedSoudy2009@gmail.com

# read DNA from fasta file
fasta <- fasta.read("virus.fasta", "host.fasta")
fasta.v <- fasta[[1]]
fasta.h <- fasta[[2]]


# Calculate ENc
enc.df.v <- ENc.values(fasta.v)

enc.df.h <- ENc.values(fasta.h)