get_pin_file

Retrieve Organism-specific PIN data

Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
'pathfindR' also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in 'pathfindR' are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR': An R Package for
Comprehensive Identification of Enriched Pathways in Omics Data Through
Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.

Ege Ulgen

pathfindR

Enrichment Analysis Utilizing Active Subnetworks

Ozan Ozisik

get_pin_file function

<dl><dt>source</dt>
<dd>As of this version, this function is implemented to get data
from 'BioGRID' only. This argument (and this wrapper function) was implemented
for future utility</dd>
<dt>org</dt>
<dd>organism name. BioGRID naming requires underscores for spaces so
'Homo sapiens' becomes 'Homo_sapiens', 'Mus musculus' becomes 'Mus_musculus'
etc. See <a href="https://wiki.thebiogrid.org/doku.php/statistics">https://wiki.thebiogrid.org/doku.php/statistics</a> for a full
list of available organisms (default = 'Homo_sapiens')</dd>
<dt>path2pin</dt>
<dd>the path of the file to save the PIN data. By default, the
PIN data is saved in a temporary file</dd>
<dt>...</dt>
<dd>additional arguments for <code>get_biogrid_pin</code></dd></dl>

Arguments

Retrieve Organism-specific PIN data — get_pin_file

<dl>

<dt>source</dt>
<dd>As of this version, this function is implemented to get data
from 'BioGRID' only. This argument (and this wrapper function) was implemented
for future utility</dd>


<dt>org</dt>
<dd>organism name. BioGRID naming requires underscores for spaces so
'Homo sapiens' becomes 'Homo_sapiens', 'Mus musculus' becomes 'Mus_musculus'
etc. See <a href='https://wiki.thebiogrid.org/doku.php/statistics'>https://wiki.thebiogrid.org/doku.php/statistics</a> for a full
list of available organisms (default = 'Homo_sapiens')</dd>


<dt>path2pin</dt>
<dd>the path of the file to save the PIN data. By default, the
PIN data is saved in a temporary file</dd>


<dt>...</dt>
<dd>additional arguments for <code>get_biogrid_pin</code></dd>

</dl>

get_pin_file: Retrieve Organism-specific PIN data

Description

Usage

Value

Arguments

Examples