create_kappa_matrix

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

create_kappa_matrix function

<dl><dt>enrichment_res</dt>
<dd>data frame of pathfindR enrichment results. Must-have
columns are 'Term_Description' (if <code>use_description = TRUE</code>) or 'ID'
(if <code>use_description = FALSE</code>), 'Down_regulated', and 'Up_regulated'.
If <code>use_active_snw_genes = TRUE</code>, 'non_Signif_Snw_Genes' must also be
provided.</dd>
<dt>use_description</dt>
<dd>Boolean argument to indicate whether term descriptions
(in the 'Term_Description' column) should be used. (default = <code>FALSE</code>)</dd>
<dt>use_active_snw_genes</dt>
<dd>boolean to indicate whether or not to use
non-input active subnetwork genes in the calculation of kappa statistics
(default = FALSE, i.e. only use affected genes)</dd></dl>

Arguments

Create Kappa Statistics Matrix — create_kappa_matrix

<dl>

<dt>enrichment_res</dt>
<dd>data frame of pathfindR enrichment results. Must-have
columns are 'Term_Description' (if <code>use_description = TRUE</code>) or 'ID'
(if <code>use_description = FALSE</code>), 'Down_regulated', and 'Up_regulated'.
If <code>use_active_snw_genes = TRUE</code>, 'non_Signif_Snw_Genes' must also be
provided.</dd>


<dt>use_description</dt>
<dd>Boolean argument to indicate whether term descriptions
(in the 'Term_Description' column) should be used. (default = <code>FALSE</code>)</dd>


<dt>use_active_snw_genes</dt>
<dd>boolean to indicate whether or not to use
non-input active subnetwork genes in the calculation of kappa statistics
(default = FALSE, i.e. only use affected genes)</dd>

</dl>

create_kappa_matrix: Create Kappa Statistics Matrix

Description

Usage

Value

Arguments

Examples