rphast (version 1.0)

simulate.msa: Simulate a MSA given a tree model and HMM.

Description

Simulate a MSA given a tree model and HMM.

Usage

simulate.msa(object, nsim, seed=NULL, hmm=NULL, get.features=FALSE,
    pointer.only=FALSE, ...)

Arguments

object

An object of type tm (or a list of these objects) describing the phylogenetic model from which to simulate. If it is a list of tree models then an HMM should be provided to describe transition rates between models.

nsim

The number of columns in the simulated alignment.

seed

A random number seed. Either NULL (the default; do not re-seed random number generator), or an integer to be sent to set.seed.

hmm

an object of type HMM describing transitions between the tree models across the columns of the alignment.

get.features

(For use with hmm). If TRUE, return object will be a list of length two. The first element will be the alignment, and the second will be an object of type feat describing the path through the phylo-hmm in the simulated alignmen

pointer.only

(Advanced use only). If TRUE, return only a pointer to the simulated alignment. Possibly useful for very (very) large alignments. Cannot be used if get.features==TRUE.

...

Currently not used (for S3 compatibility)

Value

• An object of type MSA containing the simulated alignment.

Details

Simulates a multiple sequence alignment of specified length. Deals with base-substitution only, not indels. If one tree model is given, simply simulates a sequence from this model. If an HMM is provided, then the mod parameter should be a list of tree models with the same length as the number of states in the HMM.

Examples

filename <- "rev.mod"
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
unzip(exampleArchive, filename)
m <- matrix(nrow=3, ncol=3)
m[1,] <- c(1,2,3)
m[2,] <- c(1,5,10)
m[3,] <- c(10,4,2)
eq.freq <- c(1,2,3)
h <- hmm(m, eq.freq)
mod <- read.tm(filename)
mod2 <- mod
mod2$backgd <- rep(0.25, 4)
mod3 <- mod
mod3$backgd <- c(0.6, 0.1, 0.2, 0.1)
m <- simulate.msa(mod, 20)
m <- simulate.msa(list(mod, mod2, mod3), 20, hmm=h)
m <- matrix(1, nrow=9, ncol=9)
h <- hmm(m)
m <- simulate.msa(list(mod, mod2, mod3, mod, mod2, mod3, mod, mod2, mod3),
                  20, hmm=h)
unlink(filename)