getCellProp {treekoR} | R Documentation |
getCellProp
getCellProp(phylo, clusters, samples, classes)
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 |
a dataframe containing proportions calculated for each sample
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)