example_refit_range

An example output from use of the function pred_refit_range(), applied to example gene length data and generative model fit.

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_refit_range function

A list with six entries:<dl class="dl-horizontal">
<dt>fit</dt><dd>A list with a single element 'beta', a matrix with prediction weights.</dd>
<dt>panel_genes</dt><dd>A matrix where each row corresponds to a gene,
and each entry corresponds to whether the gene is included in the panel.</dd>
<dt>panel_lengths</dt><dd>A vector giving total panel length.</dd>
</dl>

Format

Refitted Predictive Models Fitted on Example Data — example_refit_range

A list with six entries:<dl class='dl-horizontal'>
<dt>fit</dt><dd>A list with a single element 'beta', a matrix with prediction weights.</dd>
<dt>panel_genes</dt><dd>A matrix where each row corresponds to a gene,
and each entry corresponds to whether the gene is included in the panel.</dd>
<dt>panel_lengths</dt><dd>A vector giving total panel length.</dd>
</dl>

example_refit_range: Refitted Predictive Models Fitted on Example Data

Description

Usage

Arguments

Format