% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/QC_wrappers.r
\name{defineClassMarkers}
\alias{defineClassMarkers}
\title{Class markers}
\usage{
defineClassMarkers(datRef, onClasses, offClasses, numMarkers = 50)
}
\arguments{
\item{datRef}{a matrix (rows=genes x columns=samples) of gene expression data
(e.g., scRNA-seq)}

\item{onClasses}{a character (or factor) vector indicated the on class for each
sample in datRef}

\item{offClasses}{a character (or factor) vector indicated the off class for
each sample in datRef}

\item{numMarkers}{number of markers per class to return (default = 50)}
}
\value{
a 3 x count matrix of the top confused pairs of clusters with the three
  columns corresponding to mapped cluster, assigned cluster, and fraction of
  cells incorrectly mapped, respectively.
}
\description{
This function identifies both on and off markers genes for classes for use
  with patchSeqQC library. 'On markers, are genes that are highly expressed
  in the cell type of interest with enriched expression relative to other cell
  types. The second class, Off markers, are expected to be expressed at low levels
  in a given patch-seq cell type.'  Note that these markers are based on a relevant
  reference data set.
}