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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/params.R
\name{splatParams}
\alias{splatParams}
\title{Create splatParams object}
\usage{
splatParams(...)
}
\arguments{
\item{...}{parameters to set in the new params object, passed to
}
\value{
List based S3 splatParams object
}
\description{
S3 class for holding Splatter simulation parameters.
}
\details{
The splatParams object is a list based S3 object for holding simulation
parameters. It has the following sections and values:
\itemize{
\item nGenes - Number of genes to simulate.
\item nCells - Number of cells to simulate.
\item nGroups - Number of groups to simulate.
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\item [groupCells] - Vector giving the number of cells in each simulation
group/path.
\item mean (mean parameters)
\itemize{
\item rate - Rate parameter for the mean gamma simulation.
\item shape - Shape parameter for the mean gamma simulation.
}
\item lib (library size parameters)
\itemize{
\item loc - Location (meanlog) parameter for the library size
log-normal distribution.
\item scale - Scale (sdlog) parameter for the library size log-normal
distribution.
}
\item out (expression outlier parameters)
\itemize{
\item prob - Probability that a gene is an expression outlier.
\item loProb - Probability that an expression outlier gene is lowly
expressed.
\item facLoc - Location (meanlog) parameter for the expression outlier
factor log-normal distribution.
\item facScale - Scale (sdlog) parameter for the expression outlier
factor log-normal distribution.
}
\item de (differential expression parameters)
\itemize{
\item [prob] - Probability that a gene is differentially expressed
between groups or paths.
\item [downProb] - Probability that differentially expressed gene is
down-regulated.
\item [facLoc] - Location (meanlog) parameter for the differential
expression factor log-normal distribution.
\item [facScale] - Scale (sdlog) parameter for the differential
expression factor log-normal distribution.
}
\item bcv (Biological Coefficient of Variation parameters)
\itemize{
\item common - Underlying common dispersion across all genes.
\item DF - Degrees of Freedom for the BCV inverse chi-squared
distribution.
}
\item dropout (dropout parameters)
\itemize{
\item present - Logical. Whether to simulate dropout.
\item mid - Midpoint parameter for the dropout logistic function.
\item shape - Shape parameter for the dropout logistic function.
}
\item path (differentiation path parameters)
\itemize{
\item [from] - Vector giving the originating point of each path. This
allows path structure such as a cell type which differentiates
into an intermediate cell type that then differentiates into two
mature cell types. A path structure of this form would have a
"from" parameter of c(0, 1, 1) (where 0 is the origin). If no
vector is given all paths will start at the origin.
\item [length] - Vector giving the number of steps to simulate along
each path. If a single value is given it will be applied to all
paths.
\item [skew] - Vector giving the skew of each path. Values closer to 1
will give more cells towards the starting population, values
closer to 0 will give more cells towards the final population.
If a single value is given it will be applied to all paths.
\item [nonlinearProb] - Probability that a gene follows a non-linear
path along the differentiation path. This allows more complex
gene patterns such as a gene being equally expressed at the
beginning an end of a path but lowly expressed in the middle.
\item [sigmaFac] - Sigma factor for non-linear gene paths. A higher
value will result in more extreme non-linear variations along a
path.
}
}
Those shown in brackets cannot currently be easily estimated from a real
dataset by Splatter. This is also shown when a splatParams object is printed
with parameters labelled as either (estimatable) or [not estimatable].
}
\examples{
params <- splatParams()
params
}