zinbEstimate.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/zinb-estimate.R
\name{zinbEstimate}
\alias{zinbEstimate}
\alias{zinbEstimate.SingleCellExperiment}
\alias{zinbEstimate.matrix}
\title{Estimate ZINB-WaVE simulation parameters}
\usage{
zinbEstimate(counts, design.samples = NULL, design.genes = NULL,
  common.disp = TRUE, iter.init = 2, iter.opt = 25,
  stop.opt = 1e-04, params = newZINBParams(), verbose = TRUE,
  BPPARAM = SerialParam(), ...)

\method{zinbEstimate}{SingleCellExperiment}(counts,
  design.samples = NULL, design.genes = NULL, common.disp = TRUE,
  iter.init = 2, iter.opt = 25, stop.opt = 1e-04,
  params = newZINBParams(), verbose = TRUE, BPPARAM = SerialParam(),
  ...)

\method{zinbEstimate}{matrix}(counts, design.samples = NULL,
  design.genes = NULL, common.disp = TRUE, iter.init = 2,
  iter.opt = 25, stop.opt = 1e-04, params = newZINBParams(),
  verbose = TRUE, BPPARAM = SerialParam(), ...)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
containing count data to estimate parameters from.}

\item{design.samples}{design matrix of sample-level covariates.}

\item{design.genes}{design matrix of gene-level covariates.}

\item{common.disp}{logical. Whether or not a single dispersion for all
features is estimated.}

\item{iter.init}{number of iterations to use for initialization.}

\item{iter.opt}{number of iterations to use for optimization.}

\item{stop.opt}{stopping criterion for optimization.}

\item{params}{ZINBParams object to store estimated values in.}

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

\item{BPPARAM}{A \code{\link{BiocParallelParam}} instance giving the parallel
back-end to be used. Default is \code{\link{SerialParam}} which uses a
single core.}

\item{...}{additional arguments passes to \code{\link[zinbwave]{zinbFit}}.}
}
\value{
ZINBParams object containing the estimated parameters.
}
\description{
Estimate simulation parameters for the ZINB-WaVE simulation from a real
dataset.
}
\details{
The function is a wrapper around \code{\link[zinbwave]{zinbFit}} that takes
the fitted model and inserts it into a \code{\link{ZINBParams}} object. See
\code{\link{ZINBParams}} for more details on the parameters and
\code{\link[zinbwave]{zinbFit}} for details of the estimation procedure.
}
\examples{
\dontrun{
# Load example data
library(scater)
data("sc_example_counts")

params <- zinbEstimate(sc_example_counts)
params
}
}