InterCellDBPack-class: The Class for Database Storage in InterCellDB
In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

InterCellDBPack-class

R Documentation

The Class for Database Storage in InterCellDB

Description

The InterCellDBPack class provides a standard storage format of all databases for running analysis. This object is mostly created along with InterCell-class. Users need to specify the species firstly. Then, user-defined subset of database could be collected by function SelectDBSubset.

Slots

species: InterCellDB only allows 'human' and 'mouse' species.
genes.db: The gene reference database, which is generated from NCBI gene site. It records all the authorized gene names.
pairs.db: The database records all gene pairs, which are transferred from protein interaction database - 'STRING'.
actions.db: The database records all action properties (including 'action.mode', 'action.effect') for gene pairs in slot:'pairs.db'.
anno.location.db: The database collects all subcellular location from COMPARTMENTS for genes in slot:'pairs.db'.
anno.type.db: The database collects all molecular function from Uniprot for genes in slot:'pairs.db'.
go.ref.db: The database collects all GO terms for genes in slot:'pairs.db'.
accessory.db: A list of accessory database, for example, the mapping list of raw keywords from Uniport.
misc: The preserved area for miscellaneous things. Currently no usage.