psimi25Source-class: Class "psimi25Source"

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

Description

A class representing data source compatible with PSI-MI 2.5 XML data exchange format

Objects from the Class

Objects can be created by calls of the form new("psimi25Source", ...)

Slots

label:

Object of class "character", a meaningful unique label of the database, does not necessarily have to be the identifier used in the PSI-MI files. The value is advised to be overwritten by the objects

sourceDb:

Object of class "character", the character string used in the PSI-MI files to identify the source database. The value must be overwritten by the object, depending on the database identifier used in the PSI-MI file.

uniprotSymbol:

Object of class "character", the identifier of UniProf reference in "primaryRef" or "secondaryRef" attributes of the interactors, telling the parser where to find UniProt symbol of the interactors. The value must be overwritten by the objects.

Methods

sourceDb

signature(x = "psimi25Source"): returns the source database

uniprot

signature(x = "psimi25Source"): returns the uniprot identifier of the PSI-MI 2.5 XML file

Note

In case of a new data repository, you can first try creating a new object of the class with label, sourceDb and uniprotSymbol adjusted as needed. Try parsing a function with this new psimi25Source object. In case of warnings or errors, it may mean that the file provided is not strictly compatible with PSI-MI 2.5 data exchange format standard, please then contact the data provider.

Author(s)

Jitao David Zhang <[e-mail]>

See Also

parsePsimi25Interaction, parsePsimi25Complex, psimi25XML2Graph

Examples

showClass("psimi25Source")

alyst/RpsiXML documentation built on Nov. 21, 2019, 5:47 a.m.