omegaVarM4.CodonSequence: The M4 (freqs) model of variable omega ratios among sites

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

The M4 (freqs) 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 M4 (freqs) model of variable omega ratios among sites.

Distribution of omega values:

	CATEGORY	PROBABILITY

	omega_0 = 0	p0
	omega_1 = 1/3	p1
	omega_2 = 2/3	p2
	omega_3	= 1	p3
	omega_4 = 3	p4
       

Usage

## S3 method for class 'CodonSequence'
omegaVarM4(this, process, probs, index, ...)

Arguments

this	A CodonSequence object.
process	A process object inheriting from GY94.
probs	A vector of probabilities (p0 ... p4).
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

	# 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 M4
	omegaVarM4(s,p,probs=c(2/5,1/5,1/5,1/10,1/10),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.