man/SparseDCParams.Rd

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


The SparseDC simulation uses the following parameters:

\describe{
    \item{\code{nGenes}}{The number of genes to simulate in each condition.}
    \item{\code{nCells}}{The number of cells to simulate.}
    \item{\code{[seed]}}{Seed to use for generating random numbers.}
    \item{\code{markers.n}}{Number of marker genes to simulate for each
    cluster.}
    \item{\code{markers.shared}}{Number of marker genes for each cluster
    shared between conditions. Must be less than or equal to
    \code{markers.n}}.
    \item{\code{[markers.same]}}{Logical. Whether each cluster should have
    the same set of marker genes.}
    \item{\code{clusts.c1}}{Numeric vector of clusters present in
    condition 1. The number of times a cluster is repeated controls the
    proportion of cells from that cluster.}
    \item{\code{clusts.c2}}{Numeric vector of clusters present in
    condition 2. The number of times a cluster is repeated controls the
    proportion of cells from that cluster.}
    \item{\code{[mean.lower]}}{Lower bound for cluster gene means.}
    \item{\code{[mean.upper]}}{Upper bound for cluster gene means.}
}

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