% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utilities.R
\name{CollapseSpeciesExpressionMatrix}
\alias{CollapseSpeciesExpressionMatrix}
\title{Slim down a multi-species expression matrix, when only one species is primarily of interenst.}
\usage{
CollapseSpeciesExpressionMatrix(
  object,
  prefix = "HUMAN_",
  controls = "MOUSE_",
  ncontrols = 100
)
}
\arguments{
\item{object}{A UMI count matrix. Should contain rownames that start with
the ensuing arguments prefix.1 or prefix.2}

\item{prefix}{The prefix denoting rownames for the species of interest.
Default is "HUMAN_". These rownames will have this prefix removed in the returned matrix.}

\item{controls}{The prefix denoting rownames for the species of 'negative
control' cells. Default is "MOUSE_".}

\item{ncontrols}{How many of the most highly expressed (average) negative
control features (by default, 100 mouse genes), should be kept? All other
rownames starting with prefix.2 are discarded.}
}
\value{
A UMI count matrix. Rownames that started with \code{prefix} have this
prefix discarded. For rownames starting with \code{controls}, only the
\code{ncontrols} most highly expressed features are kept, and the
prefix is kept. All other rows are retained.
}
\description{
Valuable for CITE-seq analyses, where we typically spike in rare populations of 'negative control' cells from a different species.
}
\examples{
\dontrun{
cbmc.rna.collapsed <- CollapseSpeciesExpressionMatrix(cbmc.rna)
}

}
\concept{utilities}