runEdgeRTests {treekoR}R Documentation

runEdgeRTests

Description

This function runs edgeR using the treekoR inputs across all nodes of the hierarchical tree of clusters, adapted from the diffcyt workflow

Usage

runEdgeRTests(td, clusters, samples, classes, pos_class_name)

Arguments

td

a dataframe of data from ggtree object

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.

samples

a vector identifying the patient each cell belongs to

classes

a vector containing the patient outcome/class each cell belongs to

Value

a dataframe with pvalues, test statistic (signed -log10(p)), and FDR


[Package treekoR version 1.2.0 Index]