codonmat2xy: codonmat2xy

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

codonmat2xy

Description

This function calculates average behavior of each codon for all pairwise comparisons for indels, syn, and nonsyn mutations according to Nei and Gojobori (1986).

Usage

codonmat2xy(codonmat, threads = 1)

Arguments

codonmat	codon matrix obtained via dnastring2codonmat [mandatory]
threads	number of parallel threads [default: 1]

Value

A data.frame object with the following components:
Codon Codon index
n number of comparison
SynSum Sum of syn
NonSynSum Sum of nonsyn
IndelSum Sum of indels
SynMean average syn per codon
NonSynMean average nonsyn per codon
IndelMean average indels per codon
CumSumSynMean cumulative average syn per codon
CumSumNonSynMean cumulative average nonsyn per codon
CumSumIndelMean cumulative indels per codon

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

dnastring2codonmat codonmat2pnps dnastring2kaks kaks

Examples

## load example sequence data
data("hiv", package="MSA2dist")
#codonmat2xy(dnastring2codonmat(hiv))
hiv |> dnastring2codonmat() |> codonmat2xy()
#codonmat2xy(dnastring2codonmat(hiv), threads=2)
hiv |> dnastring2codonmat() |> codonmat2xy(threads=2)

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