simulateExpression.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulation.R
\name{simulateExpression}
\alias{simulateExpression}
\title{Simulation}
\usage{
simulateExpression(params = newParams(), verbose = TRUE, ...)
}
\arguments{
\item{params}{Params object containing simulation parameters for all scenarios.}

\item{verbose}{logical. Whether to print progress messages}

\item{...}{any additional parameter settings to override what is provided in \code{params}.}
}
\value{
A named list with two components: 'validationData' and 'expressionData'
}
\description{
Simulate gene expression for the different simulation scenarios: Unimodal,
multimodal with gaussian distributions, multimodal starting with a gamma distribution and followed by gaussian distributions
}
\details{
The 'modus' is the number of occurring distributions within one gene.
Modus '1' - Unimodal gaussian distribution
Gene expression for the unimodal gaussian distribution (scenario '1') is
simulated from the mean and the standard deviation taken from the validation data
for this gene. The number of values that are simulated for each
distribution equals the number of Patients {'nPatients'}:

All other modi consist of two different scenarios:
In the 'gauss' scenario all occurring distributions are gaussian distributions.
In the 'gamma' scenario the first occuring distribution is a gamma distribution.
All other distributions are gaussian distributions.

Modus '2' or higher - Bimodal distributions or higher modalities

Gene expressions of the multimodal genes are
simulated automatically for each distribution.
Scenario 'gauss'
The different gaussian distributions are simulated with the corresponding mean
and a standard deviation and number of values taken from the validation data
for this gene.

Scenario 'gamma'
The gamma distribution is simulated with the gamma shape and rate values from
the params object. The other gaussian distributions are simulated with the values
from the validation data.
}
\examples{
\dontrun{
simulation <- simulateExpression(params = newParams())
# Override default parameters
# Not recommended, better use setParams; See \\code{\\link{Params}}
simulation <- simulateExpression(nGenes = list("1"=10,
"2"=list("gauss"= 10,"gamma"= 10)), nPatients = 50)
# without messages printed to the console
params <- newParams()
simulation <- simulateExpression(params = params,verbose = FALSE)
}
}