queryPSICQUICrlib: download PSICQUIC query search result (only IMEx databases)...

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

Description

saves PSIQUIC search results to the local R library or to the directory specified

Usage

queryPSICQUICrlib(..., directory = NULL, releaseORdate = NULL,
  just_list_releases = F)

Arguments

...	Arguments passed on to queryPSICQUIC query search query in MIQL query language, as you would type in PSICQUIC View client: http://www.ebi.ac.uk/Tools/webservices/psicquic/view/home.xhtml format output format (most widely used tabular format is tab25, use tab27 for more data columns) database PSICQUIC service (full list: http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS), use "imex" shorthand to choose all IMEx databases
directory	character, directory (non-existing directory will be created) where to store the result. The default is to store the result in R library inside the PItools package
releaseORdate	character, if data has already been downloaded: which IntAct release or download date to read
just_list_releases	logical, just list IntAct releases or download dates that are locally available for this query (format: try 2017Jul12 (IntAct release) or 20170712 (download date))

Details

queryPSICQUICrlib queries IMEx databases using PSICQUIC if the local copy of the query result is not available or if there is a new IntAct release. The functions will still work for non-IMEx databases but it will check the IntAct release date and that is not meaningful for tracking updates of other resources.

Value

object of class "RAW_MItab25" or "RAW_MItab27" (list) containing 2 elements: data which is the query result (data.table) and metadata, a data.table which contains the query, the filepath, the format, the date or the IntAct release date, and the number of interactions per database

Author(s)

Vitalii Kleshchevnikov

Examples

{
queryPSICQUICrlib(query = "id:P74565 AND detmethod:\"MI:0018\"", format = "tab27", database = "imex")
}

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