.get_obs_exp

Calculates the number of expected mutations based

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

.get_obs_exp function

<dl><dt>hyp</dt>
<dd>hypothesis to be tested</dd>
<dt>select_positions</dt>
<dd>boolean column which indicates which positions are in the element of interest</dd>
<dt>dfr</dt>
<dd>a dataframe containing the data to be tested</dd>
<dt>colname</dt>
<dd>name of the column which indicates the count of mutations in the positions of interest</dd></dl>

Arguments

Calculates the number of expected mutations based — .get_obs_exp

<dl>

<dt>hyp</dt>
<dd>hypothesis to be tested</dd>


<dt>select_positions</dt>
<dd>boolean column which indicates which positions are in the element of interest</dd>


<dt>dfr</dt>
<dd>a dataframe containing the data to be tested</dd>


<dt>colname</dt>
<dd>name of the column which indicates the count of mutations in the positions of interest</dd>

</dl>

.get_obs_exp: Calculates the number of expected mutations based

Description

Usage

Value

Arguments