getCellProp {treekoR}R Documentation

getCellProp

Description

getCellProp

Usage

getCellProp(phylo, clusters, samples, classes)

Arguments

phylo

a phylogram with tip.labels corresponding to cell types/cluster contained in 'clusters' vector

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 containing proportions calculated for each sample

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")

prop_df <- getCellProp(clust_tree$clust_tree,
                        clusters=clusters,
                        samples=samples,
                        classes=classes)

[Package treekoR version 1.0.0 Index]