This function calculates pn/ps according to Nei and Gojobori (1986).
codonmat2pnps(codonmat)codon matrix of two columns to be
compared [mandatory]
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
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.
## load example sequence data
data("hiv", package="MSA2dist")
#codonmat2pnps(dnastring2codonmat(hiv)[,c(1, 2)])
(hiv |> dnastring2codonmat())[,c(1, 2)] |> codonmat2pnps()
#> seq1 seq2 Codons
#> "U68496" "U68497" "91"
#> Compared Ambigiuous Indels
#> "91" "0" "0"
#> Ns Sd Sn
#> "0" "3" "6"
#> S N ps
#> "57" "216" "0.0526315789473684"
#> pn pn/ps ds
#> "0.0277777777777778" "0.527777777777778" "0.0545695157118212"
#> dn dn/ds
#> "0.0283052459871352" "0.518700699793888"
#> attr(,"class")
#> [1] "pnps"