splat.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{splat}
\alias{splat}
\alias{splatGroups}
\alias{splatPaths}
\alias{splatSingle}
\title{Simulate scRNA-seq data}
\usage{
splat(params = defaultParams(), method = c("single", "groups", "paths"),
  verbose = TRUE, ...)

splatSingle(params = defaultParams(), verbose = TRUE, ...)

splatGroups(params = defaultParams(), verbose = TRUE, ...)

splatPaths(params = defaultParams(), verbose = TRUE, ...)
}
\arguments{
\item{params}{splatParams object containing parameters for the simulation.
See \code{\link{splatParams}} for details.}

\item{method}{which simulation method to use. Options are "single" which
produces a single population, "groups" which produces distinct groups
(eg. cell types) or "paths" which selects cells from continuous
trajectories (eg. differentiation process).}

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

\item{...}{any additional parameter settings to override what is provided in
\code{params}.}
}
\value{
SCESet object containing the simulated counts and intermediate values
}
\description{
Simulate count data from a fictional single-cell RNA-seq experiment.
}
\details{
Parameters can be set in a variety of ways. If no parameters are provided
the default parameters are used (see \code{\link{defaultParams}}). Any
parameters in \code{params} can be overridden by supplying additional
arguments through a call to \code{\link{setParams}}. Finally any parameters
the are still missing (\code{NA}) are replaced with the defaults through a
call to \code{\link{mergeParams}}. This design allows the user flexibility in
how they supply parameters and allows small adjustments without creating a
new \code{splatParams} object. See examples for a demonstration of how this
can be used.

The simulation involves the following steps:
\enumerate{
  \item Set up simulation object
  \item Simulate library sizes
  \item Simulate gene means
  \item Simulate groups/paths
  \item Simulate BCV adjusted cell means
  \item Simulate true counts
  \item Simulate dropout
  \item Create final SCESet object
}

The final output is an \code{\link{SCESet}} object that contains the
simulated counts but also the values for various intermediate steps. These
are stored in the \code{\link{phenoData}} (for cell specific information),
\code{\link{featureData}} (for gene specific information) or
\code{\link{assayData}} (for gene by cell matrices) slots. This additional
information includes:
\itemize{
  \item \code{phenoData}
    \itemize{
      \item Cell - unique cell identifier
      \item Group - the group or path the cell belongs to
      \item ExpLibSize - the expected library size for that cell
      \item Step (paths only) - how far along the path each cell is
    }
  \item \code{featureData}
    \itemize{
      \item Gene - unique gene identifier
      \item BaseGeneMean - the base expression level for that gene
      \item OutlierFactor - expression outlier factor for that gene. Values
            of 1 indicate the gene is not an expression outlier.
      \item GeneMean - expression level after applying outlier factors.
      \item DEFac[Group] - the differential expression factor for each gene
            in a particular group. Values of 1 indicate the gene is not
            differentially expressed.
      \item GeneMean[Group] - expression level of a gene in a particular
            group after applying differential expression factors.
    }
  \item \code{assayData}
    \itemize{
      \item BaseCellMeans - the expression of genes in each cell adjusted for
            expected library size.
      \item BCV - the Biological Coefficient of Variation for each gene in
            each cell.
      \item CellMeans - the expression level of genes in each cell adjusted
            for BCV.
      \item TrueCounts - the simulated counts before dropout.
      \item Dropout - logical matrix showing which values have been dropped
            in which cells.
    }
 }

 Values that have been added by Splatter are named using \code{CamelCase} in
 order to differentiate them from the values added by Scater which uses
 \code{underscore_naming}.
}
\examples{
# Simulation with default parameters
sim <- splat()
# Simulation with different number of genes
sim <- splat(nGenes = 1000)
# Simulation with custom parameters
params <- splatParams(nGenes = 100, mean.rate = 0.5)
sim <- splat(params)
# Simulation with adjusted custom parameters
sim <- splat(params, mean.rate = 0.6, out.prob = 0.2)
# Simulate paths instead of groups
sim <- splat(method = "paths")
}
\seealso{
\code{\link{addLibSizes}}, \code{\link{addGeneMeans}},
\code{\link{addSingleCellMeans}}, \code{\link{addGroupDE}},
\code{\link{addGroupCellMeans}}, \code{\link{addPathDE}},
\code{\link{addPathCellMeans}}, \code{\link{addBCVMeans}},
\code{\link{addTrueCounts}}, \code{\link{addDropout}}
}