RefNet

Description

A query interface to a large collecion of molecular interactions.

Constructor

RefNet: establishes connectin to the central PSICQUIC web server, and loads all "native" data sources.

Methods

providers(x): lists short names of the data providers

providerClasses(x): lists the names of logical groupings of the providers.

interactions(x,id, species, speciesExclusive, type, provider,detectionMethod, publicationID, quiet): retrieves all interactions matching the specified pattern.

providerClasses(x): lists the names of logical groupings of the providers.

show(x): displays current providers and related data

Functions

detectDuplicateInteractions(tbl): adds a column grouping all interactions by their two participants. The 0th dupGroup is all singletons.

pickBestFromDupGroup(dupGrr, tbl.dups, preferred.interaction.types): matches, in order, the preferred types against the interactions types, returning tbl.dups rowname for best match.

pubmedAbstract(pmid, split=FALSE): returns the text of the pubmed abstract

Author(s)

Paul Shannon

See Also

PSICQUIC, interactions, providerClasses, providers, pubmedAbstract, detectDuplicateInteractions, pickBestFromDupGroup

Examples

    # List the sources
  refNet <- RefNet()
  show(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)

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/RefNet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RefNet-class
> ### Title: RefNet
> ### Aliases: class:RefNet RefNet RefNet-class show,RefNet-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>     # List the sources
>   refNet <- RefNet()
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2016-06-06
downloading from 'https://annotationhub.bioconductor.org/fetch/10364'
retrieving 1 resource
loading from cache '/home/ddbj/.AnnotationHub/10365'
downloading from 'https://annotationhub.bioconductor.org/fetch/12810'
retrieving 1 resource
downloading from 'https://annotationhub.bioconductor.org/fetch/12814'
retrieving 1 resource
loading from cache '/home/ddbj/.AnnotationHub/27766'
loading from cache '/home/ddbj/.AnnotationHub/27767'
downloading from 'https://annotationhub.bioconductor.org/fetch/27768'
retrieving 1 resource
downloading from 'https://annotationhub.bioconductor.org/fetch/27769'
retrieving 1 resource
[1] RefNet ready.
>   show(refNet)
RefNet object with 35 providers in 2 classes
| provider class 'native':
|     gerstein-2012
|     hypoxiaSignaling-2006
|     stamlabTFs-2012
|     recon202
|     gerstein-2012
|     hypoxiaSignaling-2006
|     stamlabTFs-2012
|     recon202
| provider class 'PSICQUIC':
|     APID
|     BioGrid
|     bhf-ucl
|     ChEMBL
|     DIP
|     HPIDb
|     InnateDB
|     InnateDB-All
|     IntAct
|     mentha
|     MPIDB
|     MatrixDB
|     MINT
|     Reactome
|     Reactome-FIs
|     I2D
|     I2D-IMEx
|     InnateDB-IMEx
|     MolCon
|     UniProt
|     MBInfo
|     BindingDB
|     VirHostNet
|     Spike
|     BAR
|     EBI-GOA-nonIntAct
|     ZINC
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>