reactome.db: reactome_dbconn – R documentation

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reactome_dbconn

Collect information about the package annotation DB

Description

Some convenience functions for getting a connection object to (or collecting information about) the package annotation DB.

Usage

reactome_dbconn()
  reactome_dbfile()
  reactome_dbschema(file="", show.indices=FALSE)
  reactome_dbInfo()

Arguments

`file`	A connection, or a character string naming the file to print to (see the `file` argument of the `cat` function for the details).
`show.indices`	The CREATE INDEX statements are not shown by default. Use `show.indices=TRUE` to get them.

Details

reactome_dbconn returns a connection object to the package annotation DB. IMPORTANT: Don't call dbDisconnect on the connection object returned by reactome_dbconn or you will break all the AnnDbObj objects defined in this package!

reactome_dbfile returns the path (character string) to the package annotation DB (this is an SQLite file).

reactome_dbschema prints the schema definition of the package annotation DB.

reactome_dbInfo prints other information about the package annotation DB.

Value

reactome_dbconn: a DBIConnection object representing an open connection to the package annotation DB.

reactome_dbfile: a character string with the path to the package annotation DB.

reactome_dbschema: none (invisible NULL).

reactome_dbInfo: none (invisible NULL).

Examples

library(RSQLite)
  ## Count the number of rows in the "pathway2name" table:
  dbGetQuery(reactome_dbconn(), "SELECT COUNT(*) FROM pathway2name")

  ## The connection object returned by reactome_dbconn() was
  ## created with:
  dbConnect(SQLite(), dbname=reactome_dbfile(), cache_size=64000,
  synchronous="off")

  reactome_dbschema()

  reactome_dbInfo()

reactome.db

A set of annotation maps for reactome

v1.74.0

CC BY 4.0

Authors

Willem Ligtenberg

Initial release