Create founder haplotypes using MaCS
Uses the MaCS software to produce founder haplotypes.
runMacs( nInd, nChr = 1, segSites = NULL, inbred = FALSE, species = "GENERIC", split = NULL, ploidy = 2L, manualCommand = NULL, manualGenLen = NULL, nThreads = NULL )
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. |
The current species histories are included: GENERIC, CATTLE, WHEAT, MAIZE, and EUROPEAN.
an object of MapPop-class
# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 100 segregating sites founderPop = runMacs(nInd=10,nChr=1,segSites=100)
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