PCRcoal: The PCRcoal class

In pcrcoal: Implementing the Coalescent Approach to PCR Simulation Developed by Weiss and Von Haeseler (NAR, 1997)

Description

PCRcoal is a class implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997).

Usage

PCRcoal( initial.size, nr.cycles, efficiencies, sample.size, max.tries=100 )

Returns a PCRcoal S4 object.

Slots

initial.size:

Number of template molecules.

nr.cycles:

Number of PCR cycles.

efficiencies:

A vector of per-cycle PCR efficiencies. It is recycled if its length is smaller than nr.cycles.

sample.size:

Number of molecules sampled after amplification.

max.tries:

Maximum number of tries when sampling a size trajectory with a large enough final size.

Methods

sample.tree:

Sample a tree, return as an ape phylo object.

sample.tnt:

Return the sampled tree, subsample sizes and size trajectories in a list.

sample.trs:

Return the sampled subsample sizes and size trajectories in a list.

Note

• The original method of Weiss and von Haeseler produces a tree containing a multifurcating root node connected to the subtrees corresponding to the different subsamples. In order to be able to store the output in phylo objects, PCRcoal randomly breaks the polytomy by "coalescing" the subsample trees with zero branch lengths. Some branch length might be non-zero, in the case a subsample coalesced into one molecule which accumulated branch length ("replication count") in the previous cycles.

• If the cycle number and/or the efficiencies are small, it can happen that the number of the molecules after the amplification is less than the specified sample size. PCRcoal will try sampling size trajectories max.tries times (100 by default) to get enough amplified molecules and then aborts the simulation.

Author(s)

Botond Sipos

References

Weiss, G, von Haeseler, A (1997) A coalescent approach to the polymerase chain reaction. NAR 25(15): 3082-3087 http://dx.doi.org/10.1093/nar/25.15.3082

See Also

The ape and phylosim packages.

Examples

	# Construct a PCRcoal object 
        # and specify the experimental conditions:
        sim <-PCRcoal(
        initial.size    =5,
        sample.size     =10,
        nr.cycles       =20,
        efficiencies    =c(rep(0.1, 30))
        )

	##
	## Method: sample.tree
	##

	 # Sample a coalescent tree:
        tree <- sample.tree(sim)

        # Print tree info:
        print(tree)

        # Plot the tree:
        plot(tree)
	
	##
	## Method: sample.tnt
	##

	# Sample a coalescent tree with subsample sizes and
	# size trajectories:
        res <- sample.tnt(sim)

        # Print subsample sizes:
        print(res$subsamples)

        # Print size trajectories:
        print(res$trajectories)

        # Print tree info:
        print(res$phylo)
	
	##
	## Method: sample.trs
	##

	# Sample subsample sizes and size trajectories:
        res <- sample.trs(sim)

        # Print subsample sizes:
        print(res$subsamples)

        # Print size trajectories:
        print(res$trajectories)

	##
	## Simulating mutations using PhyloSim
	##

	# Sample tree:
	tree <- sample.tree(sim)

	# Load the phylosim package
	library(phylosim)
	# Construct a PhyloSim object, set up the root
	# sequence and the substitution process:	
	psim <- PhyloSim(
		phylo = tree,
		root.seq=sampleStates( NucleotideSequence(length=10,processes=list(list(JC69())) ) )
	)
	# Scale the tree:	
	scaleTree(psim,0.1)

	# Simulate mutations:
	Simulate(psim)

	# Plot the resulting alignment:
	plot(psim,plot.ancestors=FALSE)

pcrcoal documentation built on May 1, 2019, 8:03 p.m.