example_tmb_tables

An example output produced by using the function get_biomarker_tables(), applied to the example MAF data pre-loaded in example_maf_data$maf.

datasets

Implementation of the methodology proposed in 'Data-driven design of targeted gene panels for estimating immunotherapy biomarkers', Bradley and Cannings (2021) <arXiv:2102.04296>. This package allows the user to fit generative models of mutation from an annotated mutation dataset, and then further to produce tunable linear estimators of exome-wide biomarkers. It also contains functions to simulate mutation annotated format (MAF) data, as well as to analyse the output and performance of models.

Jacob R. Bradley

ICBioMark

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

Timothy I. Cannings

example_tmb_tables function

A list with threeobjects: 'train', 'val' and 'test'. Each is a dataframe with two columns:<dl class="dl-horizontal">
<dt>Tumor_Sample_Barcode</dt><dd>A unique ID for each sample.</dd>
<dt>TMB</dt><dd>The value of Tumour Mutation Burden for that sample.</dd>
</dl>

Format

Tumour Mutation Burden of Example Train, Validation and Test Data. — example_tmb_tables

A list with threeobjects: 'train', 'val' and 'test'. Each is a dataframe with two columns:<dl class='dl-horizontal'>
<dt>Tumor_Sample_Barcode</dt><dd>A unique ID for each sample.</dd>
<dt>TMB</dt><dd>The value of Tumour Mutation Burden for that sample.</dd>
</dl>

example_tmb_tables: Tumour Mutation Burden of Example Train, Validation and Test Data.

Description

Usage

Arguments

Format