createSimpleBimap: Creates a simple Bimap from a SQLite database in an situation...

In Bioconductor/AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor

Creates a simple Bimap from a SQLite database in an situation that is external to AnnotationDbi

Description

This function allows users to easily make a simple Bimap object for extra tables etc that they may wish to add to their annotation packages. For most Bimaps, their definition is stored inside of AnnotationDbi. The addition of this function is to help ensure that this does not become a limitation, by allowing simple extra Bimaps to easily be defined external to AnnotationDbi. Usually, this will be done in the zzz.R source file of a package so that these extra mappings can be seemlessly integrated with the rest of the package. For now, this function assumes that users will want to use data from just one table.

Usage

  createSimpleBimap(tablename, Lcolname, Rcolname, datacache, objName,
  objTarget)

Arguments

tablename	The name of the database table to grab the mapping information from.
Lcolname	The field name from the database table. These will become the Lkeys in the final mapping.
Rcolname	The field name from the database table. These will become the Rkeys in the final mapping.
datacache	The datacache object should already exist for every standard Annotation package. It is not exported though, so you will have to access it with ::: . It is needed to provide the connection information to the function.
objName	This is the name of the mapping.
objTarget	This is the name of the thing the mapping goes with. For most uses, this will mean the package name that the mapping belongs with.

Examples

##You simply have to call this function to create a new mapping.  For
##example, you could have created a mapping between the gene_name and
##the symbols fields from the gene_info table contained in the hgu95av2
##package by doing this:
library(hgu95av2.db)
hgu95av2NAMESYMBOL <- createSimpleBimap("gene_info",
                                        "gene_name",
                                        "symbol",
                                        hgu95av2.db:::datacache,
                                        "NAMESYMBOL",
                                        "hgu95av2.db")

Bioconductor/AnnotationDbi documentation built on Nov. 2, 2024, 6:27 a.m.