Lun2Params.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllClasses.R
\docType{class}
\name{Lun2Params}
\alias{Lun2Params}
\alias{Lun2Params-class}
\title{The Lun2Params class}
\description{
S4 class that holds parameters for the Lun simulation.
}
\section{Parameters}{


The Lun2 simulation uses the following parameters:

\describe{
  \item{\code{nGenes}}{The number of genes to simulate.}
  \item{\code{nCells}}{The number of cells to simulate.}
  \item{\code{[seed]}}{Seed to use for generating random numbers.}
  \item{\code{[nPlates]}}{The number of plates to simulate.}
  \item{\emph{Plate parameters}}{
    \describe{
      \item{\code{plate.ingroup}}{Character vecotor giving the plates
      considered to be part of the "ingroup".}
      \item{\code{plate.mod}}{Plate effect modifier factor. The plate effect
      variance is divided by this value.}
      \item{\code{plate.var}}{Plate effect variance.}
    }
  }
  \item{\emph{Gene parameters}}{
    \describe{
      \item{\code{gene.means}}{Mean expression for each gene.}
      \item{\code{gene.disps}}{Dispersion for each gene.}
      \item{\code{gene.ziMeans}}{Zero-inflated gene means.}
      \item{\code{gene.ziDisps}}{Zero-inflated gene dispersions.}
      \item{\code{gene.ziProps}}{Zero-inflated gene zero proportions.}
    }
  }
  \item{\emph{Cell parameters}}{
    \describe{
      \item{\code{cell.plates}}{Factor giving the plate that each cell comes
      from.}
      \item{\code{cell.libSizes}}{Library size for each cell.}
      \item{\code{cell.libMod}}{Modifier factor for library sizes.
      The library sizes are multiplied by this value.}
    }
  }
  \item{\emph{Differential expression parameters}}{
    \describe{
      \item{\code{de.nGenes}}{Number of differentially expressed genes.}
      \item{\code{de.fc}}{Fold change for differentially expressed genes.}
    }
  }
}

The parameters not shown in brackets can be estimated from real data using
\code{\link{lun2Estimate}}. For details of the Lun2 simulation see
\code{\link{lun2Simulate}}.
}