codonmat2pnps: codonmat2pnps

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

codonmat2pnps

Description

This function calculates pn/ps according to Nei and Gojobori (1986).

Usage

codonmat2pnps(codonmat)

Arguments

codonmat

codon matrix of two columns to be compared [mandatory]

Value

An object of class pnps which is a list with the following components:
seq1 sequence1 name
seq2 sequence2 name
Codons sequence2 name
Compared sequence2 name
Ambigiuous sequence2 name
Indels sequence2 name
Ns sequence2 name
Sd sequence2 name
Sn sequence2 name
S sequence2 name
N sequence2 name
ps sequence2 name
pn sequence2 name
pnps sequence2 name
ds sequence2 name
dn sequence2 name
dnds sequence2 name

Author(s)

Kristian K Ullrich

References

Nei and Gojobori. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3(5), 418-426.

Ganeshan et al. (1997) Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J. Virology. 71(1), 663-677.

Yang et al. (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155(1), 431-449.

See Also

kaks

Examples

## load example sequence data
data("hiv", package="MSA2dist")
#codonmat2pnps(dnastring2codonmat(hiv)[,c(1, 2)])
(hiv |> dnastring2codonmat())[,c(1, 2)] |> codonmat2pnps()

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.