% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_read.R

 \name{read_gmql}
 \alias{read_gmql}

 \alias{read_GRangesList}

 \title{Function read}

 \usage{

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

 read_GRangesList(samples)

 }
 \arguments{

 \item{dataset}{folder path for GMQL dataset or dataset name on repository}

 \item{parser}{string used to parsing dataset files.
 The Parsers available are:

 \itemize{

 \item{BedParser}
 \item{BroadPeakParser}

 \item{NarrowPeakParser}

 \item{CustomParser}

 }
 Default is CustomParser.}
 
 \item{is_local}{logical value indicating local or remote dataset}
 

 \item{is_GMQL}{logical value indicating GMQL dataset or not}

 \item{samples}{GRangesList}

 }
 \value{

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

 }
 \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.

 }
 \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:

 \itemize{

 \item{"provider" = "PoliMi"}
 \item{"application" = "RGMQL"}

 }

 }
 \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)

 
 }