testTree {treekoR}R Documentation

Title

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,
  pos_class_name = NULL,
  subjects = NULL,
  paired = FALSE
)

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

pos_class_name

a character indicating which class is positive

subjects

a vector containing which subject the cell belongs to, used to identify matched samples in paired t-tests (not yet tested)

paired

a boolean indicating whether to performed paired t-tests (not yet tested)

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,
                        pos_class_name=NULL,
                        subjects=NULL,
                        paired = FALSE)

[Package treekoR version 1.0.0 Index]