CodonSubst: The CodonSubst class

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

This is a class implementing a continuous-time Markov process acting on the state-space defined by the CodonAlphabet class.

The rate matrix can be built from PAML files specified by the paml.file argument. Alternatively the rates can be specified as a list through the rate.list parameter.

Package:
Class CodonSubst

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Process
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GeneralSubstitution
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--CodonSubst

Directly known subclasses:
ECMrest, ECMunrest

public static class CodonSubst
extends GeneralSubstitution

Usage

CodonSubst(name="Anonymous", paml.file=NA, rate.list=NA, equ.dist=NA, ...)

Arguments

name	The name of the object.
paml.file	The name of the PAML file used to construct the rate matrix.
rate.list	A list of unscaled substitution rates (see setRateList.GeneralSubstitution).
equ.dist	Equilibrium distribution.
...	Additional arguments.

Fields and Methods

Methods:

	buildFromPAML	-
	checkConsistency	-
	newMatrix	-
	setEquDist	-
	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

See Also

For more information see CodonSubst.

Examples

	# create an object
	p<-CodonSubst()
	# build rate matrix from paml file
	# buildFromPAML(p,"path_to_paml_file")	# do not run this
	# get object summary
	summary(p)
 

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