availableXrefs {RpsiXML} | R Documentation |
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.
availableXrefs(x,...) xref(x)
x |
for availableXrefs , 'x' can either be an object of
psimi25Interactor-class ,
link{psimi25InteractionEntry} or a list of
psimi25Interactor-class objects.
for xref , 'x' should be an object of psimi25Interactor-class
|
... |
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") hprdSet <- parsePsimi25Interaction(hprdxml, HPRD.PSIMI25) hprdInteractors <- interactors(hprdSet) availableXrefs(hprdSet) xref(hprdInteractors[[1]]) availableXrefs(hprdInteractors[[1]])