SCUO.values: Synonymous codon usage eorderliness (SCUO)

In vhcub: Virus-Host Codon Usage Co-Adaptation Analysis

Description

Measure the Synonymous Codon Usage Eorderliness (SCUO) of DNA sequence (Wan et al., 2004).

Usage

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

Arguments

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.

Details

For more information about ENc Wan et al., 2004.

Value

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

Author(s)

Ali Mostafa Anwar [e-mail] and Mohmed Soudy [e-mail]

Examples

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

# Calculate SCUO

SCUO.df <- SCUO.values(fasta.v)

vhcub documentation built on Nov. 15, 2019, 5:10 p.m.