take: Method take

In RGMQL: GenoMetric Query Language for R/Bioconductor

Description

Wrapper to TAKE operation

It saves the content of a dataset that contains samples metadata and regions as GRangesList. It is normally used to store in memory the content of any dataset generated during a GMQL query. The operation can be very time-consuming. If you invoked any materialization before take function, all those datasets are materialized as folders.

Usage

take(.data, ...)

## S4 method for signature 'GMQLDataset'
take(.data, rows = 0L)

Arguments

.data	returned object from any GMQL function
...	Additional arguments for use in other specific methods of the generic take function
rows	number of regions rows for each sample that you want to retrieve and store in memory. By default it is 0, that means take all rows for each sample

Value

GRangesList with associated metadata

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 "rd" using CustomParser

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

## This statement creates a dataset called 'aggr' which contains one 
## sample for each antibody_target and cell value found within the metadata 
## of the 'rd' dataset sample; each created sample contains all regions 
## from all 'rd' samples with a specific value for their 
## antibody_target and cell metadata attributes.
 
aggr = aggregate(rd, conds(c("antibody_target", "cell")))

## This statement performs the query and returns the resulted dataset as 
## GRangesList named 'taken'. It returns only the first 45 regions of 
## each sample present into GRangesList and all the medatata associated 
## with each sample

taken <- take(aggr, rows = 45)

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