translateID: Finds identifiers of a given object

Description Usage Arguments Details Value Author(s) See Also Examples

Description

see translateID-methods

Usage

1

Arguments

r

An object of psimi25Graph, psimi25Hypergraph, psimi25Interactor or a list of psimi25Interactor

...

the symbol of the ID to translate

Details

see translateID-methods

Value

The object of the same class as the parameter

Author(s)

Jitao David Zhang <[email protected]>

See Also

see translateID-methods

Examples

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xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")

hprdxml <- file.path(xmlDir, "hprd_200709_test.xml")
hprdSet <- parsePsimi25Interaction(hprdxml, HPRD.PSIMI25)

it <- interactors(hprdSet)[[1]]
translateID(it, "uniprot")
translateID(it, "entrezgene")

##Not run
intactxml <- file.path(xmlDir, "intact_2008_test.xml")
intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25)
intactGraph <- psimi25XML2Graph(intactxml, INTACT.PSIMI25)
intactGraphNew <- translateID(intactGraph,"sourceId")## translate the nodes of the graph to another identifier
                              
intactSetInteractors <- interactors(intactSet)
intactXrefExample <- xref(intactSetInteractors[[1]])
translateID(intactSetInteractors,"intact")
translateID(intactSetInteractors[[1]],"intact")

intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
intactComplexSet <- parsePsimi25Complex(intactComplexxml, INTACT.PSIMI25)
intactComplexGraph <- psimi25XML2Graph(intactComplexxml, INTACT.PSIMI25, type="complex")
translateID(intactComplexGraph, "intact", "P49432")
translateID(intactComplexGraph, "intact", NA)
## End(Not run)

alyst/RpsiXML documentation built on July 10, 2017, 11:46 p.m.