compute_np

main function to compute np from a user-provided expression matrix.

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

compute_np function

<dl><dt>cache</dt>
<dd>user-provided filepath for where to store data etc</dd>
<dt>experiment_name</dt>
<dd>name of the experiment for saving output.</dd>
<dt>ppi</dt>
<dd>should we use biogrid or stringdb for the PPI</dd>
<dt>min_score</dt>
<dd>if ppi is stringdb, which mininum score should we use to filter edges?</dd>
<dt>exp_mat</dt>
<dd>expression matrix where columns are samples and rows are features</dd>
<dt>mir_paper</dt>
<dd>are we running this in the context of the mir paper? a few quirks of that data</dd>
<dt>ncores</dt>
<dd>number of cores to use for calculations</dd></dl>

Arguments

main function to compute np from a user-provided expression matrix. — compute_np

<dl>

<dt>cache</dt>
<dd>user-provided filepath for where to store data etc</dd>


<dt>experiment_name</dt>
<dd>name of the experiment for saving output.</dd>


<dt>ppi</dt>
<dd>should we use biogrid or stringdb for the PPI</dd>


<dt>min_score</dt>
<dd>if ppi is stringdb, which mininum score should we use to filter edges?</dd>


<dt>exp_mat</dt>
<dd>expression matrix where columns are samples and rows are features</dd>


<dt>mir_paper</dt>
<dd>are we running this in the context of the mir paper? a few quirks of that data</dd>


<dt>ncores</dt>
<dd>number of cores to use for calculations</dd>

</dl>

compute_np: main function to compute np from a user-provided expression matrix.

Description

Usage

Value

Arguments