Evaluate Single-Cell ATAC Peak Co-Accessibility Fidelity (SCRIP)

Evaluates the preservation of chromatin peak-to-peak co-accessibility correlation matrices (cis-regulatory interactions) between reference and simulated scATAC-seq datasets.

Usage

calc_peak_coaccessibility_fidelity(
  ref_atac,
  sim_atac,
  top_n_peaks = 300,
  method = c("spearman", "pearson")
)

Arguments

ref_atac

Reference scATAC-seq matrix (peaks x cells).

sim_atac

Simulated scATAC-seq matrix (peaks x cells).

top_n_peaks

Number of highest variance peaks to evaluate (default 300).

method

Correlation method: "spearman" (default) or "pearson".

Value

A list containing RV coefficient, matrix correlation, Frobenius distance, and MAE.

Examples

data(example_scrna, package = "scSimEval")
calc_peak_coaccessibility_fidelity(example_scrna$ref, example_scrna$sim)
#> $rv_coefficient
#> [1] 0.5649862
#> 
#> $coaccessibility_pearson
#> [1] -0.01444
#> 
#> $coaccessibility_spearman
#> [1] -0.01044432
#> 
#> $frobenius_distance
#> [1] 0.005401201
#> 
#> $coaccessibility_mae
#> [1] 0.1283634
#>