match_seeds

This function will generate n character vectors of seeds to be passed to sparseRWR
as part of the construction of a boostrapped null distribution for significance testing.

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

match_seeds function

<dl><dt>g</dt>
<dd>igraph object representing the network under study. specified by "ppi" in bootstrap_null</dd>
<dt>seed_proteins</dt>
<dd>user defined seed proteins</dd>
<dt>n</dt>
<dd>number of random walks with repeats to create null distribution</dd>
<dt>set_seed</dt>
<dd>integer to set random number seed - for reproducibility</dd></dl>

Arguments

Identify random sets of seeds with similar degree distribution to parent seed proteins — match_seeds

<dl>

<dt>g</dt>
<dd>igraph object representing the network under study. specified by "ppi" in bootstrap_null</dd>


<dt>seed_proteins</dt>
<dd>user defined seed proteins</dd>


<dt>n</dt>
<dd>number of random walks with repeats to create null distribution</dd>


<dt>set_seed</dt>
<dd>integer to set random number seed - for reproducibility</dd>

</dl>

match_seeds: Identify random sets of seeds with similar degree distribution to parent seed proteins

Description

Usage

Value

Arguments