getCellProp {treekoR} | R Documentation

## getCellProp

### Description

getCellProp

### Usage

    getCellProp(phylo, clusters, samples, classes, excl_top_node_parent = TRUE)

### 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
`excl_top_node_parent` | a boolean indicating whether the for cell types with the highest node as their parent

### 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 1.2.1 Index]