Evaluate Chromatin Accessibility Profile Concordance (DiTSim)

Computes global and cell-type-stratified Pearson and Spearman correlations and Kullback-Leibler (KL) divergence between empirical reference and simulated single-cell chromatin accessibility profiles.

Usage

calc_accessibility_profile_concordance(
  ref_data,
  sim_data,
  cell_types = NULL,
  use_tfidf = TRUE
)

Arguments

ref_data

Reference count/accessibility matrix (peaks x cells).

sim_data

Simulated count/accessibility matrix (peaks x cells).

cell_types

Optional factor or vector of cell-type annotations for cells.

use_tfidf

Logical, whether to apply TF-IDF transformation prior to mean profile calculation (default TRUE).

Value

A list containing global PCC, global SCC, per-cell-type mean PCC/SCC, and mean accessibility KL divergence.

Examples

data(example_multiomics, package = "scSimEval")
r_rna <- example_multiomics$ref_multi$rna
r_atac <- example_multiomics$ref_multi$atac
calc_accessibility_profile_concordance(r_rna, r_atac)
#> $global_pcc
#> [1] 0.2982499
#> 
#> $global_scc
#> [1] 0.3483745
#> 
#> $kl_divergence
#> [1] 0.03359463
#> 
#> $mean_celltype_pcc
#> [1] NA
#> 
#> $mean_celltype_scc
#> [1] NA
#> 
#> $celltype_summary
#> NULL
#>