Last data update: 2014.03.03

 R: interactions
interactionsR Documentation

interactions

Description

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.

Usage

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

Arguments

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.

Value

A data.frame with 16 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, addStandardNames, IDMapper

Examples

  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")]

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RefNet)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: AnnotationHub
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RefNet/interactions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: interactions
> ### Title: interactions
> ### Aliases: interactions interactions,RefNet-method
> ###   S4method{interactions}{RefNet}
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   refnet <- RefNet()
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2016-06-06
loading from cache '/home/ddbj/.AnnotationHub/10364'
loading from cache '/home/ddbj/.AnnotationHub/10365'
loading from cache '/home/ddbj/.AnnotationHub/12810'
downloading from 'https://annotationhub.bioconductor.org/fetch/12814'
retrieving 1 resource
loading from cache '/home/ddbj/.AnnotationHub/27766'
downloading from 'https://annotationhub.bioconductor.org/fetch/27767'
retrieving 1 resource
downloading from 'https://annotationhub.bioconductor.org/fetch/27768'
retrieving 1 resource
loading from cache '/home/ddbj/.AnnotationHub/27769'
[1] RefNet ready.
>   providers(refnet)
$native
[1] "gerstein-2012"         "hypoxiaSignaling-2006" "stamlabTFs-2012"      
[4] "recon202"              "gerstein-2012"         "hypoxiaSignaling-2006"
[7] "stamlabTFs-2012"       "recon202"             

$PSICQUIC
 [1] "APID"              "BioGrid"           "bhf-ucl"          
 [4] "ChEMBL"            "DIP"               "HPIDb"            
 [7] "InnateDB"          "InnateDB-All"      "IntAct"           
[10] "mentha"            "MPIDB"             "MatrixDB"         
[13] "MINT"              "Reactome"          "Reactome-FIs"     
[16] "I2D"               "I2D-IMEx"          "InnateDB-IMEx"    
[19] "MolCon"            "UniProt"           "MBInfo"           
[22] "BindingDB"         "VirHostNet"        "Spike"            
[25] "BAR"               "EBI-GOA-nonIntAct" "ZINC"             

>       # 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")]
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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