ICBioMark (version 0.1.4)

get_K: Construct Bias Penalisation

Description

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

Usage

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().

Value

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

Examples

# NOT RUN {
K <- get_K(example_gen_model, 1, example_tables$train$matrix)
print(K)
# }