R/commandlineFunctions.R
simulatePhenotypes.Rd
simulatePhenotypes runs without arguments. Upon call, it reads command-line
parameters and supplies these to runSimulation
and
savePheno
. For details on input to runSimulation
and savePheno
, please refer to their help pages. For help on
the command line arguments that can be passed, see examples below. From the
command line, the help function can be called via
'Rscript -e "PhenotypeSimulator::simulatePhenotypes()" --args --help
simulatePhenotypes()
# (not run) # Simulate simple phenotype of genetic and noise background effects only: # (not run) # Rscript -e "PhenotypeSimulator::simulatePhenotypes()" \ #--args \ #--NrSamples=100 --NrPhenotypes=15 \ #--tNrSNPs=10000 --cNrSNPs=30 \ #--SNPfrequencies=0.05,0.1,0.3,0.4 \ #--genVar=0.4 --h2s=0.025 --phi=0.6 --delta=0.3 --gamma=1 \ #--pcorr=0.8 \ #--NrFixedEffects=4 --NrConfounders=1,2,1,2 \ #--pIndependentConfounders=0,1,1,0.5 \ #--distConfounders=bin,cat_norm,cat_unif,norm \ #--probConfounders=0.2 \ #--catConfounders=0,3,4,0 \ #--directory=/tmp \ #--showProgress \