.fix_all_results

fix_all_results verifies that the results table has the correct format and p-values

A method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. 'ActiveDriverWGS' detects coding and noncoding driver elements using whole genome sequencing data. The method is part of the following publication: Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Molecular Cell (2020) <doi:10.1016/j.molcel.2019.12.027>.

Juri Reimand

ActiveDriverWGS

A Driver Discovery Tool for Cancer Whole Genomes

Helen Zhu

Kevin Cheng

.fix_all_results function

<dl><dt>all_results</dt>
<dd>a data frame containing the following columns<dl>
 <dt>id</dt>
<dd>A string identifying the element of interest</dd></dl></dd> <dt>pp_element</dt>
<dd>The p-value of the element</dd> <dt>element_muts_obs</dt>
<dd>The number of patients with a mutation in the element</dd> <dt>element_muts_exp</dt>
<dd>The expected number of patients with a mutation in the element with respect to background</dd> <dt>element_enriched</dt>
<dd>A boolean indicating whether the element is enriched in mutations</dd> <dt>pp_site</dt>
<dd>The p-value of the element</dd> <dt>site_muts_obs</dt>
<dd>The number of patients with a mutation in the site</dd> <dt>site_muts_exp</dt>
<dd>The expected number of patients with a mutation in the site with respect to element</dd> <dt>site_enriched</dt>
<dd>A boolean indicating whether the site is enriched in mutations</dd> <dt>result_number</dt>
<dd>A numeric indicator denoting the order in which the results were calculated</dd>
</dl>

Arguments

fix_all_results verifies that the results table has the correct format and p-values — .fix_all_results

<dl>

<dt>all_results</dt>
<dd>a data frame containing the following columns<dl>
 <dt>id</dt>
<dd>A string identifying the element of interest</dd>

 <dt>pp_element</dt>
<dd>The p-value of the element</dd>

 <dt>element_muts_obs</dt>
<dd>The number of patients with a mutation in the element</dd>

 <dt>element_muts_exp</dt>
<dd>The expected number of patients with a mutation in the element with respect to background</dd>

 <dt>element_enriched</dt>
<dd>A boolean indicating whether the element is enriched in mutations</dd>

 <dt>pp_site</dt>
<dd>The p-value of the element</dd>

 <dt>site_muts_obs</dt>
<dd>The number of patients with a mutation in the site</dd>

 <dt>site_muts_exp</dt>
<dd>The expected number of patients with a mutation in the site with respect to element</dd>

 <dt>site_enriched</dt>
<dd>A boolean indicating whether the site is enriched in mutations</dd>

 <dt>result_number</dt>
<dd>A numeric indicator denoting the order in which the results were calculated</dd>


</dl></dd>

</dl>

.fix_all_results: fix_all_results verifies that the results table has the correct format and p-values

Description

Usage

Value

Arguments