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

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Documentation for package ‘ICBioMark’ version 0.1.4

• DESCRIPTION file.
• Package NEWS.

Help Pages

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