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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllClasses.R
\docType{class}
\name{SplatParams}
\alias{SplatParams}
\alias{SplatParams-class}
\title{The SplatParams class}
\description{
S4 class that holds parameters for the Splatter simulation.
}
\section{Parameters}{
The Splatter simulation requires the following parameters:
\describe{
\item{\code{nGenes}}{The number of genes to simulate.}
\item{\code{nCells}}{The number of cells to simulate.}
\item{\code{[nGroups]}}{The number of groups or paths to simulate.}
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\item{\code{[groupCells]}}{Vector giving the number of cells in each
simulation group/path.}
\item{\code{[seed]}}{Seed to use for generating random numbers.}
\item{\emph{Mean parameters}}{
\describe{
\item{\code{mean.shape}}{Shape parameter for the mean gamma
distribution.}
\item{\code{mean.rate}}{Rate parameter for the mean gamma
distribution.}
}
}
\item{\emph{Library size parameters}}{
\describe{
\item{\code{lib.loc}}{Location (meanlog) parameter for the library
size log-normal distribution.}
\item{\code{lib.scale}}{Scale (sdlog) parameter for the library size
log-normal distribution.}
}
}
\item{\emph{Expression outlier parameters}}{
\describe{
\item{\code{out.prob}}{Probability that a gene is an expression
outlier.}
\item{\code{out.loProb}}{Probability that an expression outlier gene
is lowly expressed.}
\item{\code{out.facLoc}}{Location (meanlog) parameter for the
expression outlier factor log-normal distribution.}
\item{\code{out.facScale}}{Scale (sdlog) parameter for the expression
outlier factor log-normal distribution.}
}
}
\item{\emph{Differential expression parameters}}{
\describe{
\item{\code{[de.prob]}}{Probability that a gene is differentially
expressed in a group. Can be a vector.}
\item{\code{[de.loProb]}}{Probability that a differentially expressed
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gene is down-regulated. Can be a vector.}
\item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
differential expression factor log-normal distribution. Can be a
vector.}
\item{\code{[de.facScale]}}{Scale (sdlog) parameter for the
differential expression factor log-normal distribution. Can be a
vector.}
}
}
\item{\emph{Biological Coefficient of Variation parameters}}{
\describe{
\item{\code{bcv.common}}{Underlying common dispersion across all
genes.}
\item{\code{bcv.df}}{Degrees of Freedom for the BCV inverse chi-squared
distribution.}
}
}
\item{\emph{Dropout parameters}}{
\describe{
\item{\code{dropout.present}}{Logical. Whether to simulate dropout.}
\item{\code{dropout.mid}}{Midpoint parameter for the dropout logistic
function.}
\item{\code{dropout.shape}}{Shape parameter for the dropout logistic
function.}
}
}
\item{\emph{Differentiation path parameters}}{
\describe{
\item{\code{[path.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{\code{[path.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{\code{[path.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{\code{[path.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{\code{[path.sigmaFac]}}{Sigma factor for non-linear gene paths.
A higher value will result in more extreme non-linear variations along
a path.}
}
}
}
The parameters not shown in brackets can be estimated from real data using
\code{\link{splatEstimate}}. For details of the Splatter simulation