union: Method union

In RGMQL: GenoMetric Query Language for R/Bioconductor

Description

Wrapper to GMQL UNION operator

It is used to integrate samples of two homogeneous or heterogeneous datasets within a single dataset; for each sample of either input dataset, a result sample is created as follows:

• Metadata are the same as in the original sample.

• Resulting schema is the schema of the left input dataset.

• Regions are the same (in coordinates and attribute values) as in the original sample, if it is from the left input dataset; if it is from the right input dataset, its regions are the same in coordinates, but only region attributes identical (in name and type) to those of the left input dataset are retained, with the same values. Region attributes which are missing in an input dataset sample w.r.t. the merged schema are set to null.

Usage

## S4 method for signature 'GMQLDataset,GMQLDataset'
union(x, y)

Arguments

x	GMQLDataset object
y	GMQLDataset object

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 folders "DATASET" and "DATASET_GDM" in the subdirectory 
## "example" of the package "RGMQL" and opens such folders as a GMQL 
## datasets named "data1" and "data2", respectively, using CustomParser

init_gmql()
test_path <- system.file("example", "DATASET", package = "RGMQL")
test_path2 <- system.file("example", "DATASET_GDM", package = "RGMQL")
data1 <- read_gmql(test_path)
data2 <- read_gmql(test_path2)

## This statement creates a dataset called 'full' which contains all samples 
## from the datasets 'data1' and 'data2'

res <- union(data1, data2)

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