vhcub (version 1.0.0)

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

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.

Value

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

Details

For more information seqinr.

Examples

# NOT RUN {
# read DNA from fasta file
fasta <- fasta.read("virus.fasta", "host.fasta")
fasta.v <- fasta[[1]]
fasta.h <- fasta[[2]]
# }
# NOT RUN {
# Calculate zscore using (codon model)
codon <- dinuc.codon(fasta.v, permutations = 10)

# }