CAI.values: Codon Adaptation Index (CAI)

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

Description

Measure the Codon Adaptation Index (CAI) Sharp and Li (1987), of DNA sequence.

Usage

CAI.values(df.virus, ENc.set.host,
                       df.host,genetic.code = "1",set.len = 5, threshold = 0)

Arguments

df.virus	a data frame with seq_name and its virus DNA sequence.
ENc.set.host	a data frame with ENc values of a host.
df.host	a data frame with seq_name and its host DNA sequence.
genetic.code	a single string that uniquely identifies a genetic code to use.
set.len	a number represents a percent that will be used as reference genes from the total host genes.
threshold	optional numeric, specifying sequence length, in codons, used for filtering.

Details

For more information about CAI Sharp and Li, 1987.

Value

A data.frame containing the computed CAI 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 CAI
enc.df.host <- ENc.values(fasta.h) 


cai.df <- CAI.values(fasta.v, enc.df.host, fasta.h)

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