simulatePhenotypes {PhenotypeSimulator}

Command line execution for PhenotypeSimulator.

Description

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

Usage

simulatePhenotypes()

Examples

# (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 \