collect: Method collect

In RGMQL: GenoMetric Query Language for R/Bioconductor

Description

Wrapper to GMQL MATERIALIZE operator

It saves the content of a dataset that contains samples metadata and regions. It is normally used to persist the content of any dataset generated during a GMQL query. Any dataset can be materialized, but the operation can be time-consuming. For best performance, materialize the relevant data only.

Usage

## S4 method for signature 'GMQLDataset'
collect(x, dir_out = getwd(), name = "ds1")

Arguments

x	GMQLDataset class object
dir_out	destination folder path. By default it is the current working directory of the R process
name	name of the result dataset. By default it is the string "ds1"

Details

An error occures if the directory already exist at the destination folder path

Value

None

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 file as a GMQL dataset named 
## "data" using CustomParser

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

## The following statement materializes the dataset 'data', previoulsy read, 
## at the specific destination test_path into local folder "ds1" opportunely 
## created

collect(data, dir_out = test_path)

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