RefNet-class: RefNet

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

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)

RefNet documentation built on April 29, 2020, 4:12 a.m.