testTree: testTree

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

testTree

Description

This function takes a hierarchical tree of the cluster medians of a cytometry dataset, and then uses this structure to perform t-tests between conditions of patients testing for difference using the proportion of cluster relative to sample's n and proportion of cluster relative to sample's n of hierarchical parent cluster. Takes a ggtree object and returns a ggtree object with testing results appended in the data

Usage

testTree(
  phylo,
  clusters,
  samples,
  classes,
  sig_test = "ttest",
  p_adjust = NULL,
  pos_class_name = NULL
)

Arguments

phylo	a 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
sig_test	a character, either "ttest" or "wilcox" indicating the significance test to be used
p_adjust	a character, indicating whether p-value adjustment should be performed. Valid values are in stats::p.adjust.methods
pos_class_name	a character indicating which class is positive

Value

a ggtree object with significance testing results in embedded data

Examples

library(SingleCellExperiment)
data(COVIDSampleData)

sce <- DeBiasi_COVID_CD8_samp
exprs <- t(assay(sce, "exprs"))
clusters <- colData(sce)$cluster_id
classes <- colData(sce)$condition
samples <- colData(sce)$sample_id

clust_tree <- getClusterTree(exprs,
                             clusters,
                             hierarchy_method="hopach")

tested_tree <- testTree(clust_tree$clust_tree,
                        clusters=clusters,
                        samples=samples,
                        classes=classes,
                        sig_test="ttest",
                        pos_class_name=NULL)

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