runMacs2 {AlphaSimR} R Documentation

## Alternative wrapper for MaCS

### Description

A wrapper function for runMacs. This wrapper is designed to provide a more intuitive interface for writing custom commands in MaCS (Chen et al. 2009). It effectively automates the creation of an appropriate line for the manualCommand argument in runMacs using user supplied variables, but only allows for a subset of the functionality offered by this argument. The default arguments of this function were chosen to match species="GENERIC" in runMacs.

### Usage

runMacs2(
nInd,
nChr = 1,
segSites = NULL,
Ne = 100,
bp = 1e+08,
genLen = 1,
mutRate = 2.5e-08,
histNe = c(500, 1500, 6000, 12000, 1e+05),
histGen = c(100, 1000, 10000, 1e+05, 1e+06),
inbred = FALSE,
split = NULL,
ploidy = 2L,
returnCommand = FALSE,
)


### Arguments

 nInd number of individuals to simulate nChr number of chromosomes to simulate segSites number of segregating sites to keep per chromosome Ne effective population size bp base pair length of chromosome genLen genetic length of chromosome in Morgans mutRate per base pair mutation rate histNe effective population size in previous generations histGen number of generations ago for effective population sizes given in histNe inbred should founder individuals be inbred split an optional historic population split in terms of generations ago ploidy ploidy level of organism returnCommand should the command passed to manualCommand in runMacs be returned. If TRUE, MaCS will not be called and the command is returned instead. nThreads if OpenMP is available, this will allow for simulating chromosomes in parallel. If the value is NULL, the number of threads is automatically detected.

### Value

an object of MapPop-class or if returnCommand is true a string giving the MaCS command passed to the manualCommand argument of runMacs.

### References

Chen GK, Marjoram P, Wall JD (2009). “Fast and Flexible Simulation of DNA Sequence Data.” Genome Research, 19, 136-142. http://genome.cshlp.org/content/19/1/136.

### Examples

# Creates a populations of 10 outbred individuals
# Their genome consists of 1 chromosome and 100 segregating sites
# The command is equivalent to using species="GENERIC" in runMacs
founderPop = runMacs2(nInd=10,nChr=1,segSites=100)



[Package AlphaSimR version 1.3.2 Index]