gfilter

Generic function to filter either an igraph object or a PPI network

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

gfilter function

<dl><dt>method</dt>
<dd>str</dd>
<dt>g</dt>
<dd>igraph object</dd>
<dt>val</dt>
<dd>named numeric vector - some measure of node state (i.e. gene expression in the case of a PPI)</dd>
<dt>use_ppi</dt>
<dd>bool - should we use a ppi from online repository?</dd>
<dt>igraph_method</dt>
<dd>bool - is the user-provided method an igraph node scoring function?</dd>
<dt>n</dt>
<dd>int - number of nodes to include in the returned subgraph</dd>
<dt>desc</dt>
<dd>bool - do we want the top or bottom examples of the provided metric</dd>
<dt>...</dt>
<dd>additional params passed to <code>load_ppi()</code> or <code>compute_crosstalk()</code></dd></dl>

Arguments

Generic function to filter either an igraph object or a PPI network — gfilter

<dl>

<dt>method</dt>
<dd>str</dd>


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


<dt>val</dt>
<dd>named numeric vector - some measure of node state (i.e. gene expression in the case of a PPI)</dd>


<dt>use_ppi</dt>
<dd>bool - should we use a ppi from online repository?</dd>


<dt>igraph_method</dt>
<dd>bool - is the user-provided method an igraph node scoring function?</dd>


<dt>n</dt>
<dd>int - number of nodes to include in the returned subgraph</dd>


<dt>desc</dt>
<dd>bool - do we want the top or bottom examples of the provided metric</dd>


<dt>...</dt>
<dd>additional params passed to <code>load_ppi()</code> or <code>compute_crosstalk()</code></dd>

</dl>

gfilter: Generic function to filter either an igraph object or a PPI network

Description

Usage

Value

Arguments

See Also