lrTest-ZlmFit-character-method.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ZlmFit.R
\name{lrTest,ZlmFit,character-method}
\alias{lrTest,ZlmFit,character-method}
\title{Likelihood ratio test}
\usage{
\S4method{lrTest}{ZlmFit,character}(object, hypothesis, ...)
}
\arguments{
\item{object}{ZlmFit}

\item{hypothesis}{See Details}

\item{...}{
  Arguments passed on to \code{\link[=zlm]{zlm}}
  \describe{
    \item{\code{formula}}{a formula with the measurement variable on the LHS and predictors present in colData on the RHS}
    \item{\code{sca}}{SingleCellAssay object}
    \item{\code{method}}{character vector, either 'glm', 'glmer' or 'bayesglm'}
    \item{\code{silent}}{Silence common problems with fitting some genes}
    \item{\code{ebayes}}{if TRUE, regularize variance using empirical bayes method}
    \item{\code{ebayesControl}}{list with parameters for empirical bayes procedure.  See \link{ebayes}.}
    \item{\code{force}}{Should we continue testing genes even after many errors have occurred?}
    \item{\code{hook}}{a function called on the \code{fit} after each gene.}
    \item{\code{parallel}}{If TRUE and \code{option(mc.cores)>1} then multiple cores will be used in fitting.}
    \item{\code{LMlike}}{if provided, then the model defined in this object will be used, rather than following the formulas.  This is intended for internal use.}
    \item{\code{onlyCoef}}{If TRUE then only an array of model coefficients will be returned (probably only useful for bootstrapping).}
    \item{\code{exprs_values}}{character or integer passed to `assay` specifying which assay to use for testing}
  }}
}
\value{
3D array
}
\description{
A 3D array with first dimension being the genes,
next dimension giving information about the test
(the degrees of freedom, Chisq statistic, and P value), and final dimension
being the value of these quantities on the
discrete, continuous and hurdle (combined) levels.
}