MSEADb: MSEADb objects

In biopackathon/MSEADbi: DBI to construct MSEA-related package

Description

MSEADb is the simple class for providing the relationship between PathBank pathway IDs and metabolite IDs contained in the pathway. It provides the database connection and easily accessible with columns, keytypes, keys and select. Some users may use additional functions such as dbconn, dbfile, dbschema, dbInfo, and species for much complex data acquisition.

columns shows which kinds of data can be returned for the MSEADb object.

keytypes allows the user to discover which keytypes can be passed in to select or keys and the keytype argument.

keys returns keys for the database contained in the MSEADb object . This method is already documented in the keys manual page but is mentioned again here because it's usage with select is so intimate. By default it will return the primary keys for the database, but if used with the keytype argument, it will return the keys from that keytype.

select will retrieve the data as a data.frame based on parameters for selected keys, columns, and keytype arguments.

dbconn returns the connection with database in the package.

dbfile returns the absolute path sqlite file is saved.

dbschema returns the database schema.

dbInfo returns the many meta information about the package.

species returns the species name.

Usage

MSEADb

Arguments

MSEADb

the MSEADb object. But in practice this will mean an object derived from an MSEADb object such as a MSEA.Ath.pb.db or many other MSEA.XXX.pb.db (XXX means abbreviation of species name).

Value

the MSEADb object

Author(s)

Kozo Nishida

See Also

dbConnect

Examples

ls("package:MSEADbi")

biopackathon/MSEADbi documentation built on Oct. 22, 2020, 12:44 p.m.