RCDI.values: Relative Codon Deoptimization Index (RCDI)

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

Description

Measure the Relative Codon Deoptimization Index (RCDI) of DNA sequence.

Usage

RCDI.values(fasta.virus, fasta.host, enc.host, set.len= 5)

Arguments

fasta.virus	a data frame with virus seq_name and its DNA sequence.
fasta.host	a data frame with host seq_name and its DNA sequence.
enc.host	a data frame of a hosts' ENc values.
set.len	a number represents a percent that will be used as reference genes from the total host genes.

Details

For more information about RCDI Puigbò et al., 2010

Value

A data.frame containing the computed ENc 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 RCDI

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


rcdi.df <- RCDI.values(fasta.v, fasta.h, enc.df.host)

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