fullInteractome: Retrieve interactome (proteins only or not) of a given...

In vitkl/MItools: Protein interaction data tools: retrieving data from IntAct and most other databases using PSICQUIC service

Description

Retrieve interactome (proteins only or not) of a given taxonomic species from a specified database. Interactome can be additionally cleaned and includes only specific information: cleanMITAB

Usage

fullInteractome(MITABdata = NULL, taxid = 9606, database = "imex",
  format = "tab25", clean = TRUE, protein_only = TRUE,
  directory = NULL, releaseORdate = NULL, remove_obsolete_id = F,
  within_species = T)

Arguments

MITABdata	object of class "RAW_MItab25" or "RAW_MItab27" (list) containing molecular interaction data as returned by queryPSICQUICrlib or loadIntActFTP, default in NULL
taxid	character (1L), taxonomy id of the species which interaction participants should belong to, default is "9606" (which is human)
database	character (1L), argument for queryPSICQUIC, PSICQUIC-compliant database to query for interactions. The default is "imex" alternative to which is "IntActFTP"
format	character (1L), argument for queryPSICQUIC, default is "tab25"
clean	logical (1L), if TRUE extract specific information using cleanMITAB, default is TRUE
protein_only	logical (1L), if TRUE the interaction participants are restricted to proteins (exclude other types of molecules such as RNA or small molecules), default is TRUE
directory	directory where to store the data, if NULL the data is stored in <R-package-library>/PItools/data
releaseORdate	character, if data has already been downloaded: which IntAct release or download date to read
remove_obsolete_id	logical (1L), remove interactions in which one of the partners is encoded as obsolete UniProtKB accession (ID), not implemented properly: will never finish.
within_species	logical (1L), return interactions only between proteins of taxid. If FALSE returns interactions for taxid proteins both within taxid and with proteins from other species

Details

taxid is used to query specified database using PSICQUIC client, only interactions in which both participants belong the taxid are retured ("taxidA:9606 AND taxidB:9606", not "species:9606"). Details: queryPSICQUIC

fullInteractome can be used to retrive interactome data using PSICQUIC service using queryPSICQUIC, clean and select specific columns using cleanMITAB and filter resulting dataset for protein-protein interaction only. This is the default option.

Alternatively, fullInteractome can only retrive interactome data using PSICQUIC service without cleaning of filtering.

Another option is to supply MITABdata to be cleaned and filtered

Finally, you can avoid using PSICQUIC service and download data from IntAct ftp by selecting database argument "IntActFTP". This is much faster but larger requires larger download (>3Gb) and is more computationally intensive for processing (clean = T). As of 7.09.2017 "IntActFTP" provides access to DIP data, while "imex" doesn't.

Value

object of class 'input class'_fullInteractome containing data.table containing molecular interaction data in either of these two formats:

if clean is TRUE: contains columns as described in cleanMITAB;

if clean is FALSE: contains a standard set of columns for MITAB2.5 or MITAB2.7 depending on format;

Author(s)

Vitalii Kleshchevnikov

See Also

interSpeciesInteractome

Examples

{
# retrive a full set of human (9606) protein-protein interactions from IMEx databases in MITAB2.5 format, clean and select specific columns (commented because takes a lot of time compared to IntActFTP)
# full = fullInteractome(taxid = "9606", database = "imex", format = "tab25", clean = TRUE, protein_only = TRUE)

# Do the same using IntAct ftp instead of the PSICQUIC webservice, except that, IntAct ftp option always outputs tab27 format
full = fullInteractome(taxid = "9606", database = "IntActFTP", clean = TRUE, protein_only = TRUE)

# retrive a full set of human (9606) protein-protein interactions from IMEx databases in MITAB2.5 format, clean and select specific columns; save it to the specific directory inside working directory
# full = fullInteractome(taxid = "9606", database = "imex", format = "tab25", clean = TRUE, protein_only = TRUE, directory = "./data/")
}

vitkl/MItools documentation built on May 29, 2019, 2:55 p.m.