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train_random_forest

Source: R/data_preparation.R
train_random_forest.Rd

Train the random forest and predict on the test sample

Usage

train_random_forest(
  res,
  df_list,
  cluster_by_res,
  sam,
  num_trees,
  verbose = 0,
  snn_graph = NULL,
  precomputed_dist = NULL,
  rf_num_threads = 1
)

Arguments

res

Resolution to train on

df_list

List containing training and test data

cluster_by_res

Named list of cluster assignment vectors, keyed by resolution (as character). Pre-extracted from training metadata using exact column names.

sam

Test sample

num_trees

Number of trees for the random forest

verbose

Integer verbosity level (0 = silent, 1 = milestones, 2 = detailed, 3 = includes Seurat output)

snn_graph

Precomputed SNN graph (sparse matrix). Required.

precomputed_dist

Optional precomputed distance matrix (output of dist). Passed through to calculate_silhouette_score.

rf_num_threads

Number of threads for ranger (default 1).

Value

A list containing the resolution, silhouette score, and number of predicted clusters.