% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/analyseTree.R
\name{runEdgeRTests}
\alias{runEdgeRTests}
\title{runEdgeRTests}
\usage{
runEdgeRTests(td, clusters, samples, classes, pos_class_name)
}
\arguments{
\item{td}{a dataframe of data from ggtree object}

\item{clusters}{a vector representing the cell type or cluster of each cell
(can be character or numeric). If numeric, cluster names need to be consecutive
starting from 1.}

\item{samples}{a vector identifying the patient each cell belongs to}

\item{classes}{a vector containing the patient outcome/class each cell belongs to}

\item{pos_class_name}{a character indicating which class should be treated as positive}
}
\value{
a dataframe with pvalues, test statistic (signed -log10(p)), and FDR
}
\description{
This function runs edgeR using the treekoR inputs across all nodes
of the hierarchical tree of clusters, adapted from the diffcyt workflow
}
