ensembl_gene_lengths

Pre-imported length data from the Ensembl database for all genes on chromosomes 1-22, X and Y.

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

ensembl_gene_lengths function

A dataframe with three columns:<dl class="dl-horizontal">
<dt>Hugo_Symbol</dt><dd>The names of all nuclear genes in humans for which ensembl entries with coding sequence lengths exist.</dd>
<dt>max_cds</dt><dd>The maximum coding sequence for each gene as given by the ensembl database.</dd>
<dt>Chromosome</dt><dd>The chromosome where each gene is located.</dd>
</dl>

Format

Gene Lengths from the Ensembl Database — ensembl_gene_lengths

A dataframe with three columns:<dl class='dl-horizontal'>
<dt>Hugo_Symbol</dt><dd>The names of all nuclear genes in humans for which ensembl entries with coding sequence lengths exist.</dd>
<dt>max_cds</dt><dd>The maximum coding sequence for each gene as given by the ensembl database.</dd>
<dt>Chromosome</dt><dd>The chromosome where each gene is located.</dd>
</dl>

ensembl_gene_lengths: Gene Lengths from the Ensembl Database

Description

Usage

Arguments

Format