Man pages for ICBioMark
Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers
| 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... |
| example_tmb_tables | Tumour Mutation Burden of Example Train, Validation and Test... |
| fit_gen_model | Fit Generative Model |
| fit_gen_model_uninteract | Fit Generative Model Without Gene/Variant Type-Specific... |
| 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... |
| 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... |
| 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... |
| vis_model_fit | Visualise Generative Model Fit |
