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prep_test

Source: R/data_preparation.R
prep_test.Rd

Prepare test data for random forest

Usage

prep_test(
  input,
  subject_ids,
  dtype = "scRNA",
  test_id,
  verbose = 0,
  residual_features = NULL
)

Arguments

input

Seurat object

subject_ids

Metadata field that identifies unique subjects.

dtype

Type of data in the Seurat object "scRNA" or "CyTOF", default is "scRNA". CyTOF data is expected to be arcsinh normalized.

test_id

subject_id for the test sample

verbose

Integer verbosity level (0 = silent, 1 = milestones, 2 = detailed, 3 = includes Seurat output, 4 = includes output from other packages such as ranger)

residual_features

Character vector of features to restrict the SCT residual computation to (passed to SCTransform(residual.features=)). Only used for scRNA data. Default NULL preserves prior behavior (residuals computed for all genes).

Value

Training data formatted for sil_score, format depends on dtype