getBridgeNames: Method to list the BridgeDb identifier mapping file names as...

In BridgeDbR: Code for using BridgeDb identifier mapping framework from within R

Description

This method returns a list of file names of BridgeDb identifier mapping files as they are available from the mapping file download site. The optional code parameter can be used to restrict the list to a specific organism.

Occassionally, the ID mapping file download website changes the pattern of the file names. In that case, you can provide an alternative filename pattern to recognize files on the download site.

This method uses data from https://bridgedb.github.io/data/gene_database/.

Usage

getBridgeNames(code, website, pattern)

Arguments

code	the organism code
website	optional parameter that allows you to provide a different location to download BridgeDb Derby files from.
pattern	optional parameter to change the filename pattern of the BridgeDb Derby files.

Value

list	the list of available BridgeDb mapping files

Author(s)

Egon Willighagen Christ Leemans

Examples

files <- getBridgeNames("Hs")
## Not run: 
prereleases <- getBridgeNames(
    website="http://bridgedb.org/data/gene_database/pre-release/",
    pattern="metabolites_\d*.bridge"
)

## End(Not run)

BridgeDbR documentation built on Nov. 8, 2020, 5:09 p.m.