getDeletionTolerance.Sequence

Sequence.getDeletionTolerance

getDeletionTolerance,Sequence-method

this

process

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

index

<p>Get 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>getParameterAtSites(this=this,process=process,id="deletion.tolerance",index=index)</code>.
	See <code>getParameterAtSites.Sequence</code> for more details.</p>

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

getDeletionTolerance.Sequence function

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

Get the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object

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

Description

Usage

Arguments

Value

See Also