kOT_sim_make

Perform optimal transport on somatic point mutations and kernel regression hypothesis testing by integrating pathway level similarities at the gene level (Little et al. (2023) <doi:10.1111/biom.13769>). The software implements balanced and unbalanced optimal transport and omnibus tests with 'C++' across a set of tumor samples and allows for multi-threading to decrease computational runtime.

Paul Little

ROKET

Optimal Transport-Based Kernel Regression

kOT_sim_make function

<dl><dt>work_dir</dt>
<dd>A full path to create "sim_ROKET" and subdirectories</dd>
<dt>NN</dt>
<dd>A positive integer for sample size</dd>
<dt>nGENE</dt>
<dd>A positive integer for number of genes to simulate</dd>
<dt>nPATH</dt>
<dd>A positive integer for number of pathways to simulate</dd>
<dt>RR</dt>
<dd>A positive integer for number of replicates to simulate</dd></dl>

Arguments

kOT_sim_make — kOT_sim_make

<dl>

<dt>work_dir</dt>
<dd>A full path to create "sim_ROKET" and subdirectories</dd>


<dt>NN</dt>
<dd>A positive integer for sample size</dd>


<dt>nGENE</dt>
<dd>A positive integer for number of genes to simulate</dd>


<dt>nPATH</dt>
<dd>A positive integer for number of pathways to simulate</dd>


<dt>RR</dt>
<dd>A positive integer for number of replicates to simulate</dd>

</dl>

kOT_sim_make: kOT_sim_make

Description

Usage

Value

Arguments