DASiR (version 1.12.0)

getDas-functions: DAS metadata information handling

Description

Functions to query metadata from the DAS server.

Usage

setDasServer(server) getDasServer() getDasSource() getDasDsn() getDasEntries(source, as.GRanges=TRUE) getDasTypes(source)

Arguments

server

URL of the DAS server.

source

The data source id to get the metadata from. Be sure this information is consistent with those returned by getDasSource. In somes cases, depending on the server, you might need to use the source title, instead of the source id.

as.GRanges

For getDasEntries, return a GRanges object instead of a data.frame (if possible).

Value

For getDasSever, getDasDsn and getDasTypes a character vectorFor getDasSource a data.frame with the information of the DBsFor getDasEntries a GRanges (as.GRanges=TRUE) or data.frame otherwise

Details

The functions documented in this man page are used to set the session's DAS server and retrieve metadata from it.

• setDasServer sets the URL of the DAS server to be used.
• getDasServer returns the URL of the DAS server used in this session
• getDasSource returns the id's, the titles and the capabilities of the data sources available in the server
• getDasDsn returns the id's of the dsn data sources available in the server
• getDasEntries returns the entry points of the given data source
• getDasTypes returns the types (a.k.a. tables) of the given data source

Please, be sure to pass the identifiers EXACTLY as the values returned by the functions available here (DAS is case-sensitive). It is also recommended that you check the capabilities for each of the data sources.

For performance reasons, the values in the main calls getDasFeature, getDasSequence, getDasStructure are not validated against the server. If you pass wrong values for source, ranges or types it will result in NULL, but no error will rise.

See Also

getDasFeature getDasSequence getDasStructure

Examples

    # Set session server to EMBL-EBI Genomic DAS Server

    setDasServer(server="http://www.ebi.ac.uk/das-srv/genomicdas/das")

    print(getDasServer())

    sources <- getDasSource()
    print(sources)

    dsn_sources <- getDasDsn()
    print(dsn_sources)

    entries <- getDasEntries(sources$id[[1]])
    print(entries)

    types <- getDasTypes(sources$id[[1]])
    print(types)