translateID: Finds identifiers of a given object

In Accio/RpsiXML: R interface to PSI-MI 2.5 files

Description

see translateID-methods

Usage

translateID(r, ...)

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 <[e-mail]>

See Also

see translateID-methods

Examples

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

hprdxml <- file.path(xmlDir, "hprd_200709_test.xml.gz")
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.gz")
intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25)
intactGraph <- psimi25XML2Graph(intactxml, INTACT.PSIMI25)
## translate the nodes of the graph to another identifier
intactGraphNew <- translateID(intactGraph,"sourceId")

intactSetInteractors <- interactors(intactSet)
intactXrefExample <- xref(intactSetInteractors[[1]])
translateID(intactSetInteractors,"intact")
translateID(intactSetInteractors[[1]],"intact")

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

Accio/RpsiXML documentation built on May 7, 2021, 12:08 a.m.