getTreeResults: getTreeResults

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

getTreeResults

Description

getTreeResults

Usage

getTreeResults(testedTree, sort_by = "parent")

Arguments

testedTree	a ggtree object outputed from testTree()
sort_by	whether to sort by p-values testing via proportions to parent or p-values testing via absolute proportions. Values can can be c(NA, "parent", "all")

Value

a dataframe with hierarchical tree nodes, corresponding clusters and corresponding significance testing results

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)

res_df <- getTreeResults(tested_tree)

head(res_df, 10)

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