Bioconductor

read_gmql

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)

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
`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"

NOTE: The folder layout must obey the following rules and adopt the following layout: The dataset folder can have any name, but must contains the sub-folders named: "files". The sub-folder "files" contains the dataset files and the schema xml file. The schema files adopt the following the naming conventions:

- "schema.xml" - "test.schema"

The names must be in LOWERCASE. Any other schema file will not be conisdered, if both are present, "test.schema" will be used.

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)

DEIB-GECO/RGMQL documentation built on Feb. 17, 2024, 10:39 p.m.