RA_clustered

A dataset containing the results of pathfindR's pathway clustering and
partitioning workflow performed on the rheumatoid arthritis
enrichment results <code>RA_output</code>. The number of clusters were detected
automatically as 8 and the agglomeration method was "average".

datasets

Pathway enrichment analysis enables researchers to uncover mechanisms
underlying the phenotype. pathfindR is a tool for pathway enrichment analysis
utilizing active subnetworks. It identifies active subnetworks in a
protein-protein interaction network using user-provided a list of genes.
It performs pathway enrichment analyses on the identified subnetworks.
pathfindR also offers functionalities to cluster enriched pathways and identify
representative pathways and to score the pathways per sample. The method is
described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R
Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv.
<doi:10.1101/272450>.

Ege Ulgen

pathfindR

Pathway Enrichment Analysis Utilizing Active Subnetworks

RA_clustered function

A data frame with 79 rows and 10 columns:<dl class="dl-horizontal">
 <dt>ID</dt><dd>KEGG ID of the enriched pathway</dd>
 <dt>Pathway</dt><dd>Description of the enriched pathway</dd>
 <dt>Fold_Enrichment</dt><dd>Fold enrichment value for the enriched pathway</dd>
 <dt>occurrence</dt><dd>the number of iterations that the given pathway was found to enriched over all iterations</dd>
 <dt>lowest_p</dt><dd>the lowest adjusted-p value of the given pathway over all iterations</dd>
 <dt>highest_p</dt><dd>the highest adjusted-p value of the given pathway over all iterations</dd>
 <dt>Up_regulated</dt><dd>the up-regulated genes in the input involved in the given pathway, comma-separated</dd>
 <dt>Down_regulated</dt><dd>the down-regulated genes in the input involved in the given pathway, comma-separated</dd>
 <dt>Cluster</dt><dd>the cluster to which the pathway is assigned</dd>
 <dt>Status</dt><dd>whether the pathway is the "Representative" pathway in its cluster or only a "Member"</dd>
</dl>

Format

Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis — RA_clustered

A data frame with 79 rows and 10 columns:<dl class='dl-horizontal'>
 <dt>ID</dt><dd>KEGG ID of the enriched pathway</dd>
 <dt>Pathway</dt><dd>Description of the enriched pathway</dd>
 <dt>Fold_Enrichment</dt><dd>Fold enrichment value for the enriched pathway</dd>
 <dt>occurrence</dt><dd>the number of iterations that the given pathway was found to enriched over all iterations</dd>
 <dt>lowest_p</dt><dd>the lowest adjusted-p value of the given pathway over all iterations</dd>
 <dt>highest_p</dt><dd>the highest adjusted-p value of the given pathway over all iterations</dd>
 <dt>Up_regulated</dt><dd>the up-regulated genes in the input involved in the given pathway, comma-separated</dd>
 <dt>Down_regulated</dt><dd>the down-regulated genes in the input involved in the given pathway, comma-separated</dd>
 <dt>Cluster</dt><dd>the cluster to which the pathway is assigned</dd>
 <dt>Status</dt><dd>whether the pathway is the "Representative" pathway in its cluster or only a "Member"</dd>
</dl>

RA_clustered: Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis

Description

Usage

Arguments

Format

See Also