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Calculate Lineage Tree Branch Height Discrepancy (RMSE)

Source: R/06_metrics_trajectory.R
calc_tree_height_discrepancy.Rd

Computes the Root Mean Squared Error (RMSE) between sorted branch heights of hierarchical lineage trees. Accepts either precomputed hclust objects OR scRNA-seq count matrices + cell_types (which will be automatically inferred).

Usage

calc_tree_height_discrepancy(
  ref_tree,
  sim_tree,
  cell_types_ref = NULL,
  cell_types_sim = NULL
)

Arguments

ref_tree

Hierarchical clustering (hclust) object from reference data, OR reference count matrix.

sim_tree

Hierarchical clustering (hclust) object from simulated data, OR simulated count matrix.

cell_types_ref

Optional cell type labels for reference (if count matrix provided).

cell_types_sim

Optional cell type labels for simulation (if count matrix provided).

Value

Root mean squared error between branch heights.

Examples

data(example_scrna, package = "scSimEval")
calc_tree_height_discrepancy(example_scrna$ref, example_scrna$sim,
                             cell_types_ref = example_scrna$cell_types,
                             cell_types_sim = example_scrna$cell_types)
#> [1] 1.867217