read-function: Function read

In RGMQL: GenoMetric Query Language for R/Bioconductor

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)

RGMQL documentation built on Nov. 8, 2020, 5:59 p.m.