getDas-functions: DAS metadata information handling
In gthar/DASiR: Distributed Annotation System in R

Description Usage Arguments Details Value Author(s) See Also Examples

Functions to query metadata from the DAS server.

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

`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).

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.

For getDasSever, getDasDsn and getDasTypes a character vector

For getDasSource a data.frame with the information of the DBs

For getDasEntries a GRanges (as.GRanges=TRUE) or data.frame otherwise

Oscar Flores <oflores@mmb.pcb.ub.es>

Anna Mantsoki <anna.mantsoki@bsc.es>

getDasFeature getDasSequence getDasStructure

    # 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)