omegaVarM3.CodonSequence: The M3 (discrete) model of variable omega ratios among sites

Description Usage Arguments Value Author(s) References See Also Examples

Description

The M3 (discrete) model of variable omega ratios among sites.

This method sets the omega site-process specific parameter in the specified range to values sampled from the M3 (discrete) model of variable omega ratios among sites.

Distribution of omega values:

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	CATEGORY	PROBABILITY

	omega_0		p0
	omega_1		p1
	omega_2 	p2
	...		...
	omega_k		pk
       

Usage

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## S3 method for class 'CodonSequence'
omegaVarM3(this, process, omegas, probs, index, ...)

Arguments

this

A CodonSequence object.

process

A process object inheriting from GY94.

omegas

A vector of omega values (omega_0 ... omega_k).

probs

A vector of probabilities (p0 ... pk).

index

A vector of positions.

...

Not used.

Value

Invisible TRUE.

Author(s)

Botond Sipos, Gregory Jordan

References

Yang, Z., Nielsen, R., Goldman, N., Pedersen Krabbe, A-M. (2000) Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites - Genetics 155:431-449 http://bit.ly/bvjucn

Goldman, N., Yang, Z. (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences - Mol Biol Evol 11(5):725-36 http://bit.ly/aSVEoa

See Also

For more information see CodonSequence.

Examples

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	# create a GY94 object
	p<-GY94(kappa=2)
	# create a CodonSequence object, attach process p
	s<-CodonSequence(length=25, processes=list(list(p)))
	# sample states
	sampleStates(s)
	# sample omegas in range 1:20 from model M3
	omegaVarM3(s,p,omegas=c(0,2,4),probs=c(1/3,1/3,1/3),1:20)
	# get omega values
	getOmegas(s,p)
	# get a histogram of omega values in range 1:20
	omegaHist(s,p,breaks=50,1:20)
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.