SiD.value: Similarity Index (SiD)

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

Description

Measure the Similarity Index (SiD) between a virus and its host codon usage.

Usage

SiD.value(rscu.host,rscu.virus)

Arguments

rscu.host	a data frame with RSCU a host codon values.
rscu.virus	a data frame with RSCU a virus codon values.

Details

For more information about SiD Zhou et al., 2013.

Value

A numeric represent a SiD value.

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]]
RSCU.H <- RSCU.values(fasta.h)
RSCU.V <- RSCU.values(fasta.v)

# Calculate SiD
SiD <- SiD.value(RSCU.host, RSCU.virus)

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