annotate_term_genes

Function to annotate the involved affected (input) genes in each term.

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

annotate_term_genes function

<dl><dt>result_df</dt>
<dd>data frame of enrichment results.
The only must-have column is 'ID'.</dd>
<dt>input_processed</dt>
<dd>input data processed via <code>input_processing</code></dd>
<dt>genes_by_term</dt>
<dd>List that contains genes for each gene set. Names of
this list are gene set IDs (default = kegg_genes)</dd></dl>

Arguments

Annotate the Affected Genes in the Provided Enriched Terms — annotate_term_genes

<dl>

<dt>result_df</dt>
<dd>data frame of enrichment results.
The only must-have column is 'ID'.</dd>


<dt>input_processed</dt>
<dd>input data processed via <code>input_processing</code></dd>


<dt>genes_by_term</dt>
<dd>List that contains genes for each gene set. Names of
this list are gene set IDs (default = kegg_genes)</dd>

</dl>

annotate_term_genes: Annotate the Affected Genes in the Provided Enriched Terms

Description

Usage

Value

Arguments

Examples