availableXrefs: Get cross reference(s) of interactors from PSI-MI 2.5 files
In Accio/RpsiXML: R interface to PSI-MI 2.5 files

Description Usage Arguments Details Value Author(s) Examples

PSI-MI 2.5 data exchange format encourages data providers to encode cross referenes of the interactors into the file, which prove valuable for annotating the data. These functions help finding out the available cross references of interactors.

1 2	availableXrefs(x,...) xref(object)

x

for availableXrefs, 'x' can either be an object of psimi25Interactor-class, link{psimi25InteractionEntry} or a list of psimi25Interactor-class objects.

for xref, 'object' should be an object of psimi25Interactor-class

object

New interface of RpsiXML uses ‘object’ uniformly.

...

intersect, logical option. If set to TRUE then only the cross references available for every interactor are returned (intersected), otherwise all the cross references are unioned and returned. See the examples

If psimi25InteractionEntry is provided as the parameter of availableXrefs, an option named "intersect" can be set to extract only those cross references intersected among all the interactors, namely the ones assigned in every interactor. Please see the examples.

`xref`	Returns a matrix with two columns: `db` (external database name) and `id` (external database index)
`availableXrefs`	A vector of characters, the names of external databases referenced in the file

Jitao David Zhang

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

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

availableXrefs(hprdSet)
xref(hprdInteractors[[1]])
availableXrefs(hprdInteractors[[1]])