providers

Description

RefNet providers are the names of data sources, many from PSICQUIC, some from RefNet.db.

Usage

## S4 method for signature 'RefNet'
providers(object)

Arguments

Value

This method returns a named list of these data sources, arrayed in two named groups, "PSICQUIC" and "native".

Author(s)

Paul Shannon

See Also

RefNet, providerClasses, interactions, addStandardNames, IDMapper

Examples

  refnet <- RefNet()
  providers(refnet)

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)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/providers.Rd_%03d_medium.png", width=480, height=480)
> ### Name: providers
> ### Title: providers
> ### Aliases: providers providers,RefNet-method S4method{providers}{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'
loading from cache '/home/ddbj/.AnnotationHub/12814'
loading from cache '/home/ddbj/.AnnotationHub/27766'
loading from cache '/home/ddbj/.AnnotationHub/27767'
loading from cache '/home/ddbj/.AnnotationHub/27768'
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"

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>