return_pin_path

<p>Name of the chosen PIN or path/to/PIN.sif. If PIN name,
must be one of c("Biogrid", "STRING", "GeneMania", "IntAct", "KEGG", "mmu_STRING"). If
path/to/PIN.sif, the file must comply with the PIN specifications. (Default = "Biogrid")</p>

pin_name_path

<p>This function returns the absolute path/to/PIN.sif. While the default PINs are
"Biogrid", "STRING", "GeneMania", "IntAct", "KEGG" and "mmu_STRING". The user can also
use any other PIN by specifying the "path/to/PIN.sif". All PINs to be used
in this package must formatted as SIF files: i.e. have 3 columns with no
header, no row names and be tab-separated. Columns 1 and 3 must be
interactors' gene symbols, column 2 must be a column with all
rows consisting of "pp".</p>

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

return_pin_path: Return The Path to Given Protein-Protein Interaction Network (PIN)

Description

Usage

Arguments

Value

See Also

Examples