dinuc.base {vhcub}

Statistical dinucleotide over- and underrepresentation (base model).

Description

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

Usage

dinuc.base(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 (base model)
base <- dinuc.base(fasta.v, permutations = 10)