RSCU.values: Relative Synonymous Codon Usage (RSCU)

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

Description

Measure the Relative Synonymous Codon Usage (RSCU) of DNA sequence.

Usage

RSCU.values(df.fasta)

Arguments

df.fasta

a data frame with seq_name and its DNA sequence.

Details

For more information about ENc Sharp et al., 1986.

Value

A data.frame containing the computed RSCU values for each codon 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 RSCU
RSCU.H <- RSCU.values(fasta.h)
RSCU.V <- RSCU.values(fasta.v)

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