omegaVarM2.CodonSequence: The M2 (selection) model of variable omega ratios among sites

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

Description

The M2 (selection) 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 M2 (selection) model of variable omega ratios among sites.

Distribution of omega values:

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	CATEGORY	PROBABILITY

	omega_0 = 0	p0
	omega_1 = 1	p1
	omega_2 	1-p0-p1
       

Usage

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## S3 method for class 'CodonSequence'
omegaVarM2(this, process, p0, p1, omega_2, index, ...)

Arguments

this

A CodonSequence object.

process

A process object inheriting from GY94.

p0

See above.

p1

See above.

omega_2

See above.

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 M2
	omegaVarM2(s,p,p0=0.2,p1=0.3,omega_2=4,1:20)
	# 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 May 19, 2017, 1:06 p.m.
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