prep_train — prep_train • clustOpt

Prepare training data for random forest

Usage

prep_train(
  input,
  subject_ids,
  dtype = "scRNA",
  within_batch = NA,
  test_id,
  verbose = 0
)

input: Seurat object
subject_ids: Metadata field that identifies unique samples.
dtype: Type of data in the Seurat object "scRNA" or "CyTOF", default is "scRNA". CyTOF data is expected to be arcsinh normalized.
within_batch: Batch variable, for a given sample only those with the same value for the batch variable will be used for training.
test_id: subject_id for the test sample
verbose: Integer verbosity level (0 = silent, 1 = milestones, 2 = detailed, 3 = includes Seurat output)

Training data formatted for sil_score, format depends on dtype