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".

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

if (FALSE) {
pin_path <- return_pin_path("GeneMania")
}