Man pages for ICBioMark
Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers

ensembl_gene_lengthsGene Lengths from the Ensembl Database
example_first_pred_tmbFirst-Fit Predictive Model Fitting on Example Data
example_gen_modelGenerative Model from Simulated Data
example_maf_dataSimulated MAF Data
example_predictionsExample Predictions
example_refit_panelRefitted Predictive Model Fitted on Example Data
example_refit_rangeRefitted Predictive Models Fitted on Example Data
example_tablesMutation Matrices from Simulated Data
example_tib_tablesTumour Indel Burden of Example Train, Validation and Test...
example_tmb_tablesTumour Mutation Burden of Example Train, Validation and Test...
fit_gen_modelFit Generative Model
fit_gen_model_uninteractFit Generative Model Without Gene/Variant Type-Specific...
fit_gen_model_unisampFit Generative Model Without Sample-Specific Effects
generate_maf_dataGenerate mutation data.
get_auprcAUPRC Metrics for Predictions
get_biomarker_from_mafProduce a Table of Biomarker Values from a MAF
get_biomarker_tablesGet True Biomarker Values on Training, Validation and Test...
get_gen_estimatesInvestigate Generative Model Comparisons
get_KConstruct Bias Penalisation
get_mutation_dictionaryGroup and Filter Mutation Types
get_mutation_tablesProduce Training, Validation and Test Matrices
get_pConstruct Optimisation Parameters.
get_panels_from_fitExtract Panel Details from Group Lasso Fit
get_predictionsProduce Predictions on an Unseen Dataset
get_r_squaredR Squared Metrics for Predictions
get_statsMetrics for Predictive Performance
get_table_from_mafProduce a Mutation Matrix from a MAF
ICBioMarkICBioMark: A package for cost-effective design of gene panels...
nsclc_mafNon-Small Cell Lung Cancer MAF Data
nsclc_survivalNon-Small Cell Lung Cancer Survival and Clinical Data
pred_first_fitFirst-Fit Predicitve Model with Group Lasso
pred_intervalsProduce Error Bounds for Predictions
pred_refit_panelRefitted Predictive Model for a Given Panel
pred_refit_rangeGet Refitted Predictive Models for a First-Fit Range of...
vis_model_fitVisualise Generative Model Fit
ICBioMark documentation built on Nov. 15, 2021, 5:09 p.m.