dinuc.codon: Statistical dinucleotide over- and underrepresentation (codon...

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

Description

A measure of statistical dinucleotide over- and underrepresentation; by allows for random sequence generation by shuffling (with/without replacement) of codons.

Usage

dinuc.codon(df.virus,permutations=500,exact_numbers = FALSE)

Arguments

df.virus	data frame with seq_name and its DNA sequence.
permutations	the number of permutations for the z-score computation.
exact_numbers	if TRUE exact analytical calculation will be used.

Details

For more information seqinr.

Value

A data.frame containing the computed statistic for each dinucleotide in all DNA sequences within df.virus.

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 zscore using (codon model)
codon <- dinuc.codon(fasta.v, permutations = 10)

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