Alternative wrapper for MaCS

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,
  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

Chen GK, Marjoram P, Wall JD (2009). “Fast and Flexible Simulation of DNA Sequence Data.” Genome Research, 19, 136-142. https://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
if (FALSE) { # \dontrun{
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)
} # }