runEdgeRTests: runEdgeRTests

In adam2o1o/treekoR: Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

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
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

adam2o1o/treekoR documentation built on June 2, 2023, 11:42 p.m.