T92: The T92 class

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

This class implements the T92 GTR-submodel.

The rate parameters are the following: "Alpha", "Beta","Gamma". The theta virtual field stores the GC content parameter.

Package:
Class T92

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Process
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GeneralSubstitution
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--UNREST
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--GTR
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--T92

Directly known subclasses:

public static class T92
extends GTR

Usage

T92(name="Anonymous", rate.params=list(Alpha = 1, Beta = 1), theta=0.5, ...)

Arguments

name	Object name.
rate.params	Rate parameters.
theta	GC content (0.5 by default).
...	Not used.

Fields and Methods

Methods:

	checkConsistency	-
	getRateParam	-
	getRateParamList	-
	getTheta	-
	setRateParam	-
	setRateParamList	-
	setTheta	-
	summary	-

Methods inherited from GTR:
checkConsistency, getBaseFreqs, getRateParam, getRateParamList, setBaseFreqs, setRateParam, setRateParamList, summary

Methods inherited from UNREST:
checkConsistency, summary

Methods inherited from GeneralSubstitution:
as.character, checkConsistency, clone, getAlphabet, getEquDist, getEventRate, getEventRateAtSite, getEventsAtSite, getQMatrix, getRate, getRateList, hasUndefinedRate, is, plot, rescaleQMatrix, sampleState, setAlphabet, setEquDist, setQMatrix, setRate, setRateList, summary

Methods inherited from Process:
!=, ==, as.character, checkConsistency, clone, getAlphabet, getEventsAtSite, getId, getName, getParameterAtSite, getSiteSpecificParamIds, getSiteSpecificParamList, getWriteProtected, hasSiteSpecificParameter, hasUndefinedRate, is, setAlphabet, setId, setName, setParameterAtSite, setSiteSpecificParamIds, setSiteSpecificParamList, setWriteProtected, summary

Methods inherited from PSRoot:
checkConsistency, enableVirtual, getComments, getMethodsList, globalConsistencyCheck, intersect.list, is, is.na, ll, my.all.equal, plot, setComments, setMethodsList, summary, virtualAssignmentForbidden

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Botond Sipos, Gregory Jordan

References

Tamura, K. (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases - Molecular Biology and Evolution 9:678-687 http://bit.ly/c6Pe0q

See Also

GTR UNREST GeneralSubstitution HKY

Examples

	# create substitution process object
       p<-T92(rate.params=list( "Alpha"=10,"Beta"=2),theta=0.8)
       # get a summary
       summary(p)
	# display a bubble plot
	plot(p)

	# The following code demonstrates how to use
	# the process in a simulation.

	# create a sequence, attach process p
	s<-NucleotideSequence(length=20,processes=list(list(p)))
	# sample states
	sampleStates(s)
	# make the first five positions invariable
	setRateMultipliers(s,p,0,1:5)
	# get rate multipliers
	getRateMultipliers(s,p)
	# create a simulation object
	sim<-PhyloSim(root.seq=s,phylo=rcoal(2))
	# run simulation
	Simulate(sim)
	# print alignment
	sim$alignment
 

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