Bioconductor

collect

R Documentation

Method collect

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, name = "ds1", dir_out = getwd())

Arguments

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

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)

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