node_repression

this function is still under development.

Provides a general toolkit for drug target identification. We include functionality to reduce large graphs to subgraphs and prioritize nodes. In addition to being optimized for use with generic graphs, we also provides support to analyze protein-protein interactions networks from online repositories. For more details on core method, refer to Weaver et al. (2021) <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008755>.

Davis Weaver

crosstalkr

Analysis of Graph-Structured Data with a Focus on
Protein-Protein Interaction Networks

node_repression function

<dl><dt>g</dt>
<dd>igraph network object</dd>
<dt>v_rm</dt>
<dd>index of vertices to remove</dd>
<dt>exp</dt>
<dd>expression vector for nodes in graph g</dd>
<dt>state_function</dt>
<dd>function to use to calculate network state before and after node_repression</dd>
<dt>neighbors_only</dt>
<dd>logical designating whether state function should be calculated for all nodes or just neighbors</dd>
<dt>...</dt>
<dd>additional parameters passed to state function.</dd></dl>

Arguments

Function to eliminate a node from a network g and calculate the change in some measure of network state — node_repression

<dl>

<dt>g</dt>
<dd>igraph network object</dd>


<dt>v_rm</dt>
<dd>index of vertices to remove</dd>


<dt>exp</dt>
<dd>expression vector for nodes in graph g</dd>


<dt>state_function</dt>
<dd>function to use to calculate network state before and after node_repression</dd>


<dt>neighbors_only</dt>
<dd>logical designating whether state function should be calculated for all nodes or just neighbors</dd>


<dt>...</dt>
<dd>additional parameters passed to state function.</dd>

</dl>

node_repression: Function to eliminate a node from a network g and calculate the change in some measure of network state

Description

Usage

Arguments