get_K function

Construct Bias Penalisation

An internal function, producing the correct bias penalisation for use in predictive model fitting.

get_K(
  gen_model,
  p_norm,
  training_matrix,
  marker_training_values = NULL,
  method = max
)

Arguments

• gen_model: (list) A generative mutation model, fitted by fit_gen_model().
• p_norm: (numeric) Scaling factor between coefficients of p and parameters of generative model (see paper for details).
• training_matrix: (sparse matrix) A sparse matrix of mutations in the training dataset, produced by get_mutation_tables().
• marker_training_values: (dataframe) A dataframe containing training values for the biomarker in question.
• method: (function) How to select a representative biomarker value from the training dataset. Defaults to max().

Returns

A numerical value, to be used as a penalty weighting in the subsequent group lasso optimisation.

Examples

K <- get_K(example_gen_model, 1, example_tables$train$matrix)
print(K)