setDeletionTolerance.Sequence

Sequence.setDeletionTolerance

setDeletionTolerance,Sequence-method

this

process

A numeric vector, recycled if shorter than the index vector.

value

An integer vector specifying a set of positions. It is set to 1:seq$length if omitted.

index

Set the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object.
	This method does some error checking and the calls <code>setParameterAtSites(this=this,process=process,id="deletion.tolerance",value=value,index=index)</code>.
	See <code>setParameterAtSites.Sequence</code> for more details.

An extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions. Citation: Botond Sipos, Tim Massingham, Gregory E Jordan and Nick Goldman (2011) PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment <doi:10.1186/1471-2105-12-104>.

Botond Sipos

phylosim

Flexible Simulations of Biological Sequence Evolution

setDeletionTolerance.Sequence function

Set the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object — setDeletionTolerance.Sequence

setDeletionTolerance.Sequence: Set the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object

Description

Usage

Arguments

Value

See Also