get_network_matrix

get_network_matrix,pathway-method

<code>get_network_matrix</code> creates the adjacency matrix representing the gene-gene interaction structure within a particular <code>pathway</code>. Note that a 
KEGG kgml file is downloaded and saved in the working directory.

Methods to extract information on pathways, genes and various single-nucleotid polymorphisms (SNPs) from online databases. It provides functions for data preparation and evaluation of genetic influence on a binary outcome using the logistic kernel machine test (LKMT). Three different kernel functions are offered to analyze genotype information in this variance component test: A linear kernel, a size-adjusted kernel and a network-based kernel (Friedrichs et al., 2017, <doi:10.1155/2017/6742763>).

Juliane Manitz

kangar00

Kernel Approaches for Nonlinear Genetic Association Regression

get_network_matrix function

<dl><dt>object</dt>
<dd>A <code>pathway</code> object identifying the pathway for which gene interaction infomation should be extracted. Here, KEGG IDs of format 'hsa00100' are used and information is downloaded from the KEGG database.</dd>
<dt>directed</dt>
<dd>A <code>logical</code> argument, stating whether the network matrix 
should return directed (<code>TRUE</code>) or undirected (<code>FALSE</code>) links.</dd>
<dt>method</dt>
<dd>Download method to be used for downloading files, passed to via <code>KEGGgraph::retrieveKGML</code> to <code><a href="/link/utils%3A%3Adownload.file?package=kangar00&version=1.4.1" data-mini-rdoc="kangar00::utils::download.file">utils::download.file</a></code> function. Currently supports <code>'auto'</code> (default), <code>'internal'</code>, <code>'wininet'</code> (Windows only), <code>'libcurl'</code>, <code>'wget'</code> and <code>'curl'</code>.</dd></dl>

Arguments

Stefanie Friedrichs, Patricia Burger, Juliane Manitz

Author

Function to calculate the network matrix for a pathway object — get_network_matrix

<dl>

<dt>object</dt>
<dd>A <code>pathway</code> object identifying the pathway for which gene interaction infomation should be extracted. Here, KEGG IDs of format 'hsa00100' are used and information is downloaded from the KEGG database.</dd>


<dt>directed</dt>
<dd>A <code>logical</code> argument, stating whether the network matrix 
should return directed (<code>TRUE</code>) or undirected (<code>FALSE</code>) links.</dd>


<dt>method</dt>
<dd>Download method to be used for downloading files, passed to via <code>KEGGgraph::retrieveKGML</code> to <code><a href='https://rdrr.io/r/utils/download.file.html'>utils::download.file</a></code> function. Currently supports <code>'auto'</code> (default), <code>'internal'</code>, <code>'wininet'</code> (Windows only), <code>'libcurl'</code>, <code>'wget'</code> and <code>'curl'</code>.</dd>

</dl>

get_network_matrix: Function to calculate the network `matrix` for a `pathway` object

Description

Usage

Value

Arguments

Author