read_gmql {RGMQL} | R Documentation

## Function read

### Description

It reads a GMQL dataset, as a folder containing some homogenus samples on disk or as a GRangesList, saving it in Scala memory in a way that can be referenced in R. It is also used to read a repository dataset in case of remote processing.

### Usage

    read_gmql(dataset, parser = "CustomParser", is_local = TRUE,
      is_GMQL = TRUE)

    read_GRangesList(samples)

### Arguments

`dataset` | folder path for GMQL dataset or dataset name on repository
`parser` | string used to parsing dataset files. The Parsers available are: BedParser BroadPeakParser NarrowPeakParser CustomParser Default is CustomParser.
`is_local` | logical value indicating local or remote dataset
`is_GMQL` | logical value indicating GMQL dataset or not
`samples` | GRangesList

### Details

Normally, a GMQL dataset contains an XML schema file that contains name of region attributes. (e.g chr, start, stop, strand) The CustomParser reads this XML schema; if you already know what kind of schema your files have, use one of the parsers defined, without reading any XML schema.

If GRangesList has no metadata: i.e. metadata() is empty, two metadata are generated:

- "provider" = "PoliMi"

- "application" = "RGMQL"

### Value

GMQLDataset object. It contains the value to use as input for the subsequent GMQLDataset method

### Examples

    ## This statement initializes and runs the GMQL server for local execution
    ## and creation of results on disk. Then, with system.file() it defines
    ## the path to the folder "DATASET" in the subdirectory "example"
    ## of the package "RGMQL" and opens such folder as a GMQL dataset
    ## named "data" using CustomParser

    init_gmql()
    test_path <- system.file("example", "DATASET", package = "RGMQL")
    data = read_gmql(test_path)

    ## This statement opens such folder as a GMQL dataset named "data" using
    ## "NarrowPeakParser"
    dataPeak = read_gmql(test_path,"NarrowPeakParser")

    ## This statement reads a remote public dataset stored into GMQL system
    ## repository. For a public dataset in a (remote) GMQL repository the
    ## prefix "public." is needed before dataset name

    remote_url = "http://www.gmql.eu/gmql-rest/"
    login_gmql(remote_url)
    data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)

[Package RGMQL version 1.4.1 Index]