webBrowser-functions: Web Browser Functions
In PSICQUIC: Proteomics Standard Initiative Common QUery InterfaCe

Description Usage Details Value Author(s) See Also Examples

PSICQUIC uses standard codes to identify species, detection methods, and interaction types. In the absence of easy-to-use data files which we could store with, and provide from this package, we instead offer methods which drive your web browser to pages which offer the relevant information.

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interactionTypes()
detectionMethods()
speciesIDs()

interactionTypes will drive your web browser to a EMBL-EBI Ontology Lookup Service devoted to protein-protein interaction types.

detectionMethods will drive your web browser to a EMBL-EBI Ontology Lookup Service devoted to protein interaction detection methods.

speciesIDs helps in finding the NCBI taxon ids which are used to identify species (e.g., "9606" for Homo sapiens). This method drives your web browser to the NCBI Taxonomy Browser (the NCBI Taxonomy Homepage), where you can use the search facilities to obtain the taxon id for your organism/s of interest.

None

Paul Shannon

providers, interactions, rawQuery, addGeneInfo, IDMapper,

  ## Not run: 
    psicquic <- PSICQUIC()
    speciesIDs()
    interactionTypes()
    detectionMethods()
    
## End(Not run)

Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

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The following objects are masked from ‘package:base’:

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    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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Loading required package: biomaRt
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Loading required package: plyr

Attaching package: ‘plyr’

The following object is masked from ‘package:IRanges’:

    desc

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Warning message:
replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’ 
Warning message:
In .loadRegistry() :
  failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
sh: 1: xdg-open: Permission denied
sh: 1: xdg-open: Permission denied
sh: 1: xdg-open: Permission denied