iRefR (version 1.13)

get_irefindex: Get iRefIndex

Description

Get a given distribution of the iRefIndex database from the ftp site.

"iRefIndex" is one of the main efforts to consolidate the information coming from different protein interaction databases in one single repository avoiding redundant information. It has been defined as "an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, Mpact, MPPI and OPHID... This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein".

Usage

get_irefindex(tax_id, iref_version, data_folder)

Arguments

tax_id

Taxon ID of the organism ("10090" for mouse, "10116" for rat, "4932" for S.Cerevisiae, "562" for E.Coli, "6239" for C.Elegans, "7227" for D.Melanogaster, "9606" for H.Sapiens, and "All" for all organisms). Default="All".

iref_version

iRefIndex distribution ("7.0", "8.0", "9.0", "10.0", "11.0", "12.0", "13.0" or "current"). Default="current".

data_folder

Folder to save the iRefIndex flat file: type "data" to save it in the "iRefR/data" directory, "home" to save it in the "R.home()" directory, or any other destination folder. Default=getwd().

Value

irefindex_tab

R Table (data frame) containing the desired iRefIndex distribution.

Examples

     ## execute function
     irefindex_13_ecoli = get_irefindex(tax_id="562", iref_version="13.0", data_folder=
 tempdir())