% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/diff-exp.R
\name{markersBinom}
\alias{markersBinom}
\title{Test for differential gene expression in two populations using a binomial test}
\usage{
markersBinom(
  object,
  pseudotime,
  clust.1 = NULL,
  clust.2 = NULL,
  cells.1 = NULL,
  cells.2 = NULL,
  clustering = NULL,
  effect.size = log(2),
  p.thresh = 0.01,
  frac.must.express = 0.1,
  genes.use = NULL
)
}
\arguments{
\item{object}{An URD object}

\item{pseudotime}{(Character)}

\item{clust.1}{(Character)}

\item{clust.2}{(Character)}

\item{cells.1}{(Character vector)}

\item{cells.2}{(Character vector)}

\item{clustering}{(Character) Name of a clustering (i.e. a column in \code{@group.ids})}

\item{effect.size}{(Numeric) Minimum log fold-change for two genes to be considered differentially expressed}

\item{p.thresh}{(Numeric) Minimum significance value for teo genes to be considered expressed}

\item{frac.must.express}{(Numeric) Gene must be expressed in at least this fraction of cells in one of the two clusters to be considered.}

\item{genes.use}{(Character vector) Genes to compare, default is NULL (all genes)}
}
\value{
(data.frame)
}
\description{
Test for differential gene expression in two populations using a binomial test
}
\references{
Shekhar et al., 2016, Cell 166, 1308â€“1323
}
