getDasFeature: Query for features to session's DAS server

Description

This function retrieves information for the features for the given ranges and types using the corresponding data source id (or title) in the session's DAS server.

Usage

getDasFeature(source, ranges, types)

Arguments

source

Data source id (or title). See getDasSource.

ranges

GRanges object containing the seqname(s) and range(s) to query. Be sure that this information is coherent with those returned by getDasEntries.

types

Names of the features to retrieve. They must match one or more of the values returned by getDasTypes.

Value

data.frame with the following columns:

id, start, stop,
    version, label, type, method, score, orientation, phase, note, link,
    target, parent, part

, which match the contents of the specific annotation for the given ranges and types in the server (some of the fields are optional, so not all the servers provide information for all the above columns).If there are not matching results, output is NULL.

Details

This function queries the DAS server and returns the available information for the type(s) at the given range(s).

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.

Please, notice that this function codes the parameters in a URL to query the server. This function could fail if you ask for many ranges or types. Also, notice that the speed of the query depends on the number of elements and the load in the server.

Please, use this function smartly and do not overload servers.

Examples

Run this code

    # Set session server to UniProt DAS Reference Server

    setDasServer(server="http://www.ebi.ac.uk/das-srv/uniprot/das")
    source <- "uniprot-summary"
    ranges <- GRanges(seqnames=c("A0A000","A0A001"), IRanges(start=c(1,1), end=c(394,591)))
    types <- c("description", "sequence-summary")

    features <- getDasFeature(source, ranges, types)
    print(features)