configure_output_dir

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

configure_output_dir function

<dl><dt>output_dir</dt>
<dd>the directory to be created where the output and intermediate
files are saved (default = <code>NULL</code>, a temporary directory is used)</dd></dl>

Arguments

Configure Output Directory Name — configure_output_dir

<dl>

<dt>output_dir</dt>
<dd>the directory to be created where the output and intermediate
files are saved (default = <code>NULL</code>, a temporary directory is used)</dd>

</dl>

configure_output_dir: Configure Output Directory Name

Description

Usage

Value

Arguments