ensembl_gene_lengths |
Gene Lengths from the Ensembl Database |
example_first_pred_tmb |
First-Fit Predictive Model Fitting on Example Data |
example_gen_model |
Generative Model from Simulated Data |
example_maf_data |
Simulated MAF Data |
example_predictions |
Example Predictions |
example_refit_panel |
Refitted Predictive Model Fitted on Example Data |
example_refit_range |
Refitted Predictive Models Fitted on Example Data |
example_tables |
Mutation Matrices from Simulated Data |
example_tib_tables |
Tumour Indel Burden of Example Train, Validation and Test Data. |
example_tmb_tables |
Tumour Mutation Burden of Example Train, Validation and Test Data. |
fit_gen_model |
Fit Generative Model |
fit_gen_model_uninteract |
Fit Generative Model Without Gene/Variant Type-Specific Interactions |
fit_gen_model_unisamp |
Fit Generative Model Without Sample-Specific Effects |
generate_maf_data |
Generate mutation data. |
get_auprc |
AUPRC Metrics for Predictions |
get_biomarker_from_maf |
Produce a Table of Biomarker Values from a MAF |
get_biomarker_tables |
Get True Biomarker Values on Training, Validation and Test Sets |
get_gen_estimates |
Investigate Generative Model Comparisons |
get_K |
Construct Bias Penalisation |
get_mutation_dictionary |
Group and Filter Mutation Types |
get_mutation_tables |
Produce Training, Validation and Test Matrices |
get_p |
Construct Optimisation Parameters. |
get_panels_from_fit |
Extract Panel Details from Group Lasso Fit |
get_predictions |
Produce Predictions on an Unseen Dataset |
get_r_squared |
R Squared Metrics for Predictions |
get_stats |
Metrics for Predictive Performance |
get_table_from_maf |
Produce a Mutation Matrix from a MAF |
ICBioMark |
ICBioMark: A package for cost-effective design of gene panels to predict exome-wide biomarkers. |
nsclc_maf |
Non-Small Cell Lung Cancer MAF Data |
nsclc_survival |
Non-Small Cell Lung Cancer Survival and Clinical Data |
pred_first_fit |
First-Fit Predicitve Model with Group Lasso |
pred_intervals |
Produce Error Bounds for Predictions |
pred_refit_panel |
Refitted Predictive Model for a Given Panel |
pred_refit_range |
Get Refitted Predictive Models for a First-Fit Range of Panels |
vis_model_fit |
Visualise Generative Model Fit |