return_pin_path: Return The Path to Given Protein-Protein Interaction Network...

In egeulgen/pathfindR: Enrichment Analysis Utilizing Active Subnetworks

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

Description

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'.

Usage

return_pin_path(pin_name_path = "Biogrid")

Arguments

pin_name_path

Name of the chosen PIN or absolute/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')

Value

The absolute path to chosen PIN.

See Also

See run_pathfindR for the wrapper function of the pathfindR workflow

Examples

## Not run: 
pin_path <- return_pin_path('GeneMania')

## End(Not run)

egeulgen/pathfindR documentation built on Feb. 1, 2024, 4:34 a.m.