Calculate Intraclass Correlation Coefficient (ICC) (hierarchicell & rescueSim)

Computes the one-way random effects Intraclass Correlation Coefficient (ICC) per gene across donors or biological replicates to quantify hierarchical clustering.

Usage

calc_intraclass_correlation(counts, donor_labels, n_genes = 200)

Arguments

counts

Matrix (genes x cells) or SingleCellExperiment.

donor_labels

Vector or factor of donor / subject IDs.

n_genes

Number of top variable genes to evaluate (default 200).

Value

A list with median ICC, mean ICC, and vector of per-gene ICC values.

Examples

data(example_scrna, package = "scSimEval")
calc_intraclass_correlation(example_scrna$ref, example_scrna$sim)
#> $median_icc
#> [1] 0
#> 
#> $mean_icc
#> [1] 0
#> 
#> $gene_icc
#>  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [39] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>