Evaluate Gene Co-Expression Module Fidelity (ESCO)

Automatically discovers or evaluates co-expression modules and measures the preservation of intra-module vs. inter-module correlation structure.

Usage

calc_coexpression_module_fidelity(
  ref_mat,
  sim_mat,
  modules = NULL,
  n_modules = 5,
  top_genes = 200
)

Arguments

ref_mat

Reference gene expression matrix (genes x cells).

sim_mat

Simulated gene expression matrix (genes x cells).

modules

Optional named list of gene modules. If NULL, auto-detected via hierarchical clustering.

n_modules

Number of modules to detect if modules is NULL (default 5).

top_genes

Number of top variable genes to consider for clustering (default 200).

Value

A list summarizing module correlation preservation, RMSE, and modularity ratio fidelity.

Examples

data(example_scrna, package = "scSimEval")
calc_coexpression_module_fidelity(example_scrna$ref, example_scrna$sim)
#> $module_correlation_r
#> [1] -0.01457616
#> 
#> $module_correlation_rmse
#> [1] 0.1690945
#> 
#> $module_correlation_mae
#> [1] 0.1360054
#> 
#> $ref_modularity_ratio
#> [1] 0.5568422
#> 
#> $sim_modularity_ratio
#> [1] -0.02798568
#> 
#> $modularity_fidelity
#> [1] 0
#>