DiscreteDeletor: The DiscreteDeletor class
In phylosim: Flexible Simulations of Biological Sequence Evolution

Description Usage Arguments Fields and Methods Author(s) See Also Examples

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

Directly known subclasses:

public static class DiscreteDeletor
extends GeneralDeletor

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

`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.

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

Botond Sipos, Gregory Jordan

GeneralDeletor ContinuousDeletor GeneralInDel

	# 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