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

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

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.

Usage

## S3 method for class 'msa'
simulate(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. Currently only models of order zero are supported, and if multiple models are given, they are currently assumed to have the same topology.
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 alignment.
pointer.only	(Advanced use only). If TRUE, return only a pointer to the simulated alignment. Possibly useful for very (very) large alignments.
...	Currently not used (for S3 compatibility)

Value

An object of type MSA containing the simulated alignment.

Note

Currently only supports HMMs in which the models for each state have the same topologies.

Author(s)

Melissa J. Hubisz and Adam Siepel

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=3, ncol=3)
h <- hmm(m)
l <- simulate.msa(list(mod, mod2, mod3), 100, get.features=TRUE, hmm=h)
names(l)
l$msa
l$feats
coverage.feat(l$feats[l$feats$feature=="state1",])
unlink(filename)

rphast documentation built on May 1, 2019, 9:26 p.m.