rawQuery: rawQuery

In paul-shannon/PSICQUIC: Proteomics Standard Initiative Common QUery InterfaCe

Description

For exploratory situations, or by personal preference, one can bypass the interactions API (which we expect will be used by most people most of the time). The rawQuery method allows you to craft your own MIQL (molecular interaction query language) query but without needing to obtain per-provider URLs. The sixteen columns of data are returned in a data.frame without column titles.

Usage

## S4 method for signature 'PSICQUIC'
rawQuery(object, provider, rawArgs)

Arguments

object	a PSICQUIC object.
provider	a character object, one of the approximately two dozen PSCIQUIC-compliant services.
rawArgs	A character string which follows MIQL syntax, which is defined here: http://code.google.com/p/psicquic/wiki/MiqlReference27 The encoding of special characters (spaces and parentheses in particular) is handled by this method, so there is no need to replace, for instance, spaces or parens with their url-safe hex codes.

Value

A data.frame with 15 columns, and one row for every interaction, described as an annotated A/B relationship, with self-describing column names.

Author(s)

Paul Shannon

See Also

providers, interactions, addGeneInfo, IDMapper, interactionTypes, detectionMethods, speciesIDs

Examples

    psicquic <- PSICQUIC()
    providers <- providers(psicquic)

       # query BioGrid for all known ALK interactions

    if("BioGrid" %in% providers){
        tbl.1 <- rawQuery(psicquic, providers[1], "identifier:ALK AND species:9606")
          # what publications?
        table(tbl.1$V8)
        }

      # query the iRefIndex provider for interactions between
      # two specified ids.  then further contrain by publication.

    if("iRefIndex" %in% providers){
       rawArgs.1 <- "identifier:(ALK AND MAP3K3) AND species:9606"
       tbl.2 <- rawQuery(psicquic, "iRefIndex", rawArgs.1)
       rawArgs.2 <- paste(rawArgs.1, " AND pubid:(15657099 OR 14743216)", sep="")
       tbl.3 <- rawQuery(psicquic, "iRefIndex", rawArgs.2)
       }

paul-shannon/PSICQUIC documentation built on May 29, 2019, 7:35 a.m.