get_positivePPI: Fetch Positive Reference Host-Pathogen Protein-Protein...

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

Fetch Positive Reference Host-Pathogen Protein-Protein Interactions (HP-PPIs) from the BioGRID Database

Description

This function retrieves positive reference host-pathogen protein-protein interactions directly from BioGRID database.

Usage

get_positivePPI(
  organism.taxID,
  access.key,
  filename = "PositiveInt.RData",
  path = "PositiveInt"
)

Arguments

organism.taxID	Taxonomy identifier for the pathogen.
access.key	Access key for using BioGRID webpage. To retrieve interactions from the BioGRID database, the users are first required to register for access key at https://webservice.thebiogrid.org/.
filename	A character string, indicating the output filename as an RData object to store the retrieved interactions.
path	A character string indicating the path to the project directory that contains the interaction data. If the directory is missing, it will be stored in the current directory. Default is PositiveInt.

Details

get_positivePPI

Value

A Data.frame containing true positive protein-protein interactions for the selected pathogen.

Author(s)

Matineh Rahmatbakhsh, [e-mail]

See Also

See get_negativePPI for generating negative protein-protein interaction.

Examples

local = tempdir()
try(get_positivePPI(organism.taxID = 2697049,
access.key = 'XXXX',
filename = "PositiveInt.RData",
path = local))

mrbakhsh/HPiP documentation built on March 28, 2023, 4:35 p.m.