prep_stringdb

Basically a wrapper around the get_graph method from the stringdb package

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

prep_stringdb function

<dl><dt>cache</dt>
<dd>A filepath to a folder downloaded files should be stored</dd>
<dt>edb</dt>
<dd>ensemble database object</dd>
<dt>min_score</dt>
<dd>minimum connectivity score for each edge in the network.</dd>
<dt>version</dt>
<dd>stringdb version</dd>
<dt>species</dt>
<dd>species code either using latin species name or taxon id</dd></dl>

Arguments

Prepare Stringdb for use in analyses — prep_stringdb

<dl>

<dt>cache</dt>
<dd>A filepath to a folder downloaded files should be stored</dd>


<dt>edb</dt>
<dd>ensemble database object</dd>


<dt>min_score</dt>
<dd>minimum connectivity score for each edge in the network.</dd>


<dt>version</dt>
<dd>stringdb version</dd>


<dt>species</dt>
<dd>species code either using latin species name or taxon id</dd>

</dl>

prep_stringdb: Prepare Stringdb for use in analyses

Description

Usage

Value

Arguments