runMacs2: Alternative wrapper for MaCS

In AlphaSimR: Breeding Program Simulations

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 \insertCiteMaCSAlphaSimR. 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,
  nThreads = NULL
)

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

\insertAllCited

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
## Not run: 
founderPop = runMacs2(nInd=10,nChr=1,segSites=100)

# runMacs() Implementation of the cattle demography following
#  Macleod et al. (2013) https://doi.org/10.1093/molbev/mst125
cattleChrSum = 2.8e9 # https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002263795.3/
(cattleChrBp = cattleChrSum / 30)
recRate = 9.26e-09
(cattleGenLen = recRate * cattleChrBp)
mutRate = 1.20e-08
runMacs2(nInd = 10, nChr = 1, Ne = 90, bp = cattleChrBp,
         genLen = cattleGenLen, mutRate = 1.20e-08,
         histNe  = c(120, 250, 350, 1000, 1500, 2000, 2500, 3500, 7000, 10000, 17000, 62000),
         histGen = c(  3,   6,  12,   18,   24,  154,  454,  654, 1754,  2354,  3354, 33154),
         returnCommand = TRUE)

## End(Not run)

AlphaSimR documentation built on Nov. 1, 2024, 5:07 p.m.