runMacs: Create founder haplotypes using MaCS

In AlphaSimR: Breeding Program Simulations

Create founder haplotypes using MaCS

Description

Uses the MaCS software to produce founder haplotypes \insertCiteMaCSAlphaSimR.

Usage

runMacs(
  nInd,
  nChr = 1,
  segSites = NULL,
  inbred = FALSE,
  species = "GENERIC",
  split = NULL,
  ploidy = 2L,
  manualCommand = NULL,
  manualGenLen = NULL,
  nThreads = NULL
)

Arguments

nInd	number of individuals to simulate
nChr	number of chromosomes to simulate
segSites	number of segregating sites to keep per chromosome. A value of NULL results in all sites being retained.
inbred	should founder individuals be inbred
species	species history to simulate. See details.
split	an optional historic population split in terms of generations ago.
ploidy	ploidy level of organism
manualCommand	user provided MaCS options. For advanced users only.
manualGenLen	user provided genetic length. This must be supplied if using manualCommand. If not using manualCommand, this value will replace the predefined genetic length for the species. However, this the genetic length is only used by AlphaSimR and is not passed to MaCS, so MaCS still uses the predefined genetic length. For advanced users only.
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.

Details

There are currently three species histories available: GENERIC, CATTLE, WHEAT, and MAIZE.

The GENERIC history is meant to be a reasonable all-purpose choice. It runs quickly and models a population with an effective populations size that has gone through several historic bottlenecks. This species history is used as the default arguments in the runMacs2 function, so the user should examine this function for the details of how the species is modeled.

The CATTLE history is based off of real genome sequence data \insertCitecattleAlphaSimR.

The WHEAT \insertCitegaynor_2017AlphaSimR and MAIZE \insertCitehickey_2014AlphaSimR histories have been included due to their use in previous simulations. However, it should be noted that neither faithfully simulates its respective species. This is apparent by the low number of segregating sites simulated by each history relative to their real-world analogs. Adjusting these histories to better represent their real-world analogs would result in a drastic increase to runtime.

Value

an object of MapPop-class

References

\insertAllCited

Examples

# Creates a populations of 10 outbred individuals
# Their genome consists of 1 chromosome and 100 segregating sites
## Not run: 
founderPop = runMacs(nInd=10,nChr=1,segSites=100)

## End(Not run)

AlphaSimR documentation built on Nov. 2, 2023, 6:01 p.m.