phylosim (version 3.0.5)

DiscreteDeletor: The DiscreteDeletor class

Description

This class implements a process which performs deletions with lengths sampled from a user-specified discrete distribution. See GeneralDeletor for how the deletion process works.

Package: Class DiscreteDeletor

Object ~~| ~~+--PSRoot ~~~~~~~| ~~~~~~~+--Process ~~~~~~~~~~~~| ~~~~~~~~~~~~+--GeneralInDel ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--GeneralDeletor ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--DiscreteDeletor

Directly known subclasses:

public static class DiscreteDeletor extends GeneralDeletor

Usage

DiscreteDeletor(name="Anonymous", rate=NA, sizes=NA, probs=NA, ...)

Arguments

name

The name of the object.

rate

The general rate.

sizes

The deletion sizes to propose.

probs

A vector with the probabilites of the deletion sizes.

...

Additional arguments.

Fields and Methods

Methods:

	checkConsistency	-
	getProbs	-
	getSizes	-
	plot	-
	setProbs	-
	setSizes	-
	summary	-

Methods inherited from GeneralDeletor: checkConsistency, getEventsAtSite, is, summary

Methods inherited from GeneralInDel: checkConsistency, getAcceptBy, getProposeBy, getRate, hasUndefinedRate, is, proposeLength, setAcceptBy, setProposeBy, setRate, 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

See Also

GeneralDeletor ContinuousDeletor GeneralInDel

Examples

# NOT RUN {
	# create a DiscreteDeletor process
	d<-DiscreteDeletor(
		name="M.D.",
		rate=0.25,
		sizes=c(1,2),
		probs=c(1/2,1/2)
 	)
	# get object summary
	summary(d)
	# set/get deletions sizes
	d$sizes<-1:3
	d$sizes
	# set/get length probabilities
	d$probs<-c(3,2,1)/6
	d$probs
	# plot length distribution
	plot(d)

	# The following code illustrates how to use
	# a DiscreteDeletor process in a simulation

	# create a sequence object, attach process d
	s<-NucleotideSequence(string="AAAAAAAAAAGGGGAAAAAAAAAA",processes=list(list(d)))
	# set the deletion tolerance to zero in the range 11:15
	# creating a region rejecting all deletions
	setDeletionTolerance(s,d,0,11:15)
	# get deletion tolerances
	getDeletionTolerance(s,d)
	# create a simulation object
	sim<-PhyloSim(root.seq=s,phylo=rcoal(2))
	# simulate
	Simulate(sim)
	# print resulting alignment
	sim$alignment
 
# }