pathfindR (version 1.2.3)

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

Description

This function returns the path/to/PIN.sif. While the default PINs are Biogrid, GeneMania, IntAct and KEGG, the user can choose to use any other PIN by specifying the path/to/PIN.sif. All PINs to be used in this workflow must have 3 columns with no header and be tab-separated. Columns 1 and 3 must be interacting proteins' HGNC 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 path/to/PIN.sif. If PIN name, must be one of c("Biogrid", "GeneMania", "IntAct", "KEGG"). If path/to/PIN.sif, the file must comply with the PIN specifications. Defaults to "Biogrid".

Value

A character value that contains the 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("Biogrid")
pin_path <- return_pin_path("KEGG")
# }