interactions: interactions
In RefNet: A queryable collection of molecular interactions, from many sources

Description Usage Arguments Value Author(s) See Also Examples

This is the primary interface to the RefNet services, in which approximately thirty interaction providers return annotated molecular (often protein-protein) interactions in response to a standard query language ("MIQL" – the molecular interaction query language). This method is thus an R interface to MIQL, with several conveniences added.

In the most typical and basic use, one specifies a species and a gene symbol, and RefNet returns a data.frame listing all of the interactions for that gene (or the protein it encodes) from all RefNet providers, of all interaction types and all detection methods.

More focused queries are easily accomplished: all arguments (execpt for the RefNet object the method dispatches on) are optional, and each specified argument limits the search space: to one or more genes, a publication identifier (typically a pubmed id), interaction types, a detection methods, and/or one or more species.

In principle you could obtain all interactions, of all types, from all providers, by using default values for all of the search-constraining arugments. But this would be very unwise! Highly specific or exploratory queries of modest scope are encouraged, as are bulk downloads using ftp directed at the providers' web sites for acquiring large interaction datasets.

## S4 method for signature 'RefNet'
interactions(object,
                                  id=NA,
                                  species=NA,
                                  speciesExclusive=TRUE,
                                  type=NA,
                                  provider=NA,
                                  detectionMethod=NA,
                                  publicationID=NA,
                                  quiet=TRUE)

`object`	a `RefNet` object.
`id`	one or more `character` strings. These are most often gene symbols (e.g., "RAD17"), to which most of the RefNet providers respond, translating these into the native identifiers of their data store, which is typically a protein identifier of one sort or another. You may also provide such a protein identifier directly (e.g., uniprot "O75943", or refseq "NP_002684"). Protein identifiers typically return fewer interactions, presumably because providers do not translate them into their native identifiers, and only a subset of the providers find matches. If multiple ids are supplied, then only interactions which occur between any two of the ids is returned. If only one id is supplied, all interactions are reported in which that id participates.
`species`	One or more `character` strings. Use an NCBI taxon code, for which the `speciesIds` method is useful. Note the next argument.
`speciesExclusive`	a `logical` variable, default TRUE. If set to FALSE than interactions will be included with proteins from species other than those explicitly named. Infection and transgenic experiments are examples of cross-species protein-protein interactions. We anticipate that the most common query seeks interactions among proteins in the same cell of the same organism. For this reason, this argument defaults to TRUE.
`type`	a `list` of `character` strings. See the method `interactionTypes`.
`provider`	a `list` of `character` strings. See the method `providers` for the currently available set. This argument defaults to NA, and all currently live providers are queried.
`detectionMethod`	a `list` of `character` strings. See the method `detectionMethods`
`publicationID`	a `list` of `character` strings. Usually a pubmedID, but sometimes an OMIM reference number.
`quiet`	a `logical` of `character` strings, default TRUE. Set to FALSE if you wish to trace the exection of your query against all providers, and explore the details of the REST API.

A data.frame with 16 columns, and one row for every interaction, described as an annotated A/B relationship, with self-describing column names.

Paul Shannon

providers, addStandardNames, IDMapper

  refnet <- RefNet()
  providers(refnet)
      # query all providers for all known Myc interactions
  tbl.1 <- interactions(refnet, id="Myc", species="9606",
                        provider="gerstein-2012")

      # all Myc/EP400 interactions known to BioGrid
      # make sure that BioGrid is currently available

  if("BioGrid" %in% providers(refnet))
     tbl.2 <- interactions(refnet, c("Myc", "EP400"), species="9606",
                           provider="BioGrid")

      # or those between Myc and any other molecule, detected by
      # the "pull down" proteomics technique and judged to be
      # a "direct interaction"

  # recon2 temporarily unavailable.  will be added to AnnotationHub soon
  # tbl.3 <- interactions(refnet, "L-alanine transaminase",  provider="recon2")
  # tbl.3[, c("A.common", "type", "B.common", "A.canonical", "B.canonical")]