nsclc_survival

A pre-loaded clinical dataset containing survival and clinical data from Campbell et. al (2016), downloaded from The Cancer Genome Atlas.

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

nsclc_survival function

An annotated mutation dataframe with 23 columns and 1144 rows. Each row
corresponds to a sample, and details clinical and survival information about the
patient from whom the sample was derived. Its columns are as follows:<dl class="dl-horizontal">
<dt>CASE_ID</dt><dd></dd>
<dt>AGE</dt><dd></dd>
<dt>AGE_AT_SURGERY</dt><dd></dd>
<dt>CANCER_TYPE</dt><dd></dd>
<dt>CANCER_TYPE_DETAILED</dt><dd></dd>
<dt>DAYS_TO_DEATH</dt><dd></dd>
<dt>DAYS_TO_LAST_FOLLOWUP</dt><dd></dd>
<dt>FRACTION_GENOME_ALTERED</dt><dd></dd>
<dt>HISTORY_NEOADJUVANT_TRTYN</dt><dd></dd>
<dt>HISTORY_OTHER_MALIGNANCY</dt><dd></dd>
<dt>MUTATION_COUNT</dt><dd></dd>
<dt>M_STAGE</dt><dd></dd>
<dt>N_STAGE</dt><dd></dd>
<dt>ONCOTREE_CODE</dt><dd></dd>
<dt>OS_MONTHS</dt><dd></dd>
<dt>OS_STATUS</dt><dd></dd>
<dt>SAMPLE_COUNT</dt><dd></dd>
<dt>SEX</dt><dd></dd>
<dt>SMOKING_HISTORY</dt><dd></dd>
<dt>SMOKING_PACK_YEARS</dt><dd></dd>
<dt>SOMATIC_STATUS</dt><dd></dd>
<dt>STAGE</dt><dd></dd>
<dt>T_STAGE</dt><dd></dd>
</dl>

Format

Non-Small Cell Lung Cancer Survival and Clinical Data — nsclc_survival

An annotated mutation dataframe with 23 columns and 1144 rows. Each row
corresponds to a sample, and details clinical and survival information about the
patient from whom the sample was derived. Its columns are as follows:<dl class='dl-horizontal'>
<dt>CASE_ID</dt><dd></dd>
<dt>AGE</dt><dd></dd>
<dt>AGE_AT_SURGERY</dt><dd></dd>
<dt>CANCER_TYPE</dt><dd></dd>
<dt>CANCER_TYPE_DETAILED</dt><dd></dd>
<dt>DAYS_TO_DEATH</dt><dd></dd>
<dt>DAYS_TO_LAST_FOLLOWUP</dt><dd></dd>
<dt>FRACTION_GENOME_ALTERED</dt><dd></dd>
<dt>HISTORY_NEOADJUVANT_TRTYN</dt><dd></dd>
<dt>HISTORY_OTHER_MALIGNANCY</dt><dd></dd>
<dt>MUTATION_COUNT</dt><dd></dd>
<dt>M_STAGE</dt><dd></dd>
<dt>N_STAGE</dt><dd></dd>
<dt>ONCOTREE_CODE</dt><dd></dd>
<dt>OS_MONTHS</dt><dd></dd>
<dt>OS_STATUS</dt><dd></dd>
<dt>SAMPLE_COUNT</dt><dd></dd>
<dt>SEX</dt><dd></dd>
<dt>SMOKING_HISTORY</dt><dd></dd>
<dt>SMOKING_PACK_YEARS</dt><dd></dd>
<dt>SOMATIC_STATUS</dt><dd></dd>
<dt>STAGE</dt><dd></dd>
<dt>T_STAGE</dt><dd></dd>
</dl>

nsclc_survival: Non-Small Cell Lung Cancer Survival and Clinical Data

Description

Usage

Arguments

Format