cover-param-class: PARAM object class constructor

In RGMQL: GenoMetric Query Language for R/Bioconductor

Description

This class constructor is used to create instances of PARAM object to be used in GMQL cover method

Usage

ALL()

ANY()

Details

• ALL: It represents the number of samples in the input dataset.

• ANY: It represents any amount of overlapping regions to be considered.

Value

Param object

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 file "DATASET" in the subdirectory "example"
## of the package "RGMQL" and opens such file as a GMQL dataset named "exp" 
## using CustomParser

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

## The following statement produces an output dataset with a single 
## output sample. The COVER operation considers all areas defined by 
## a minimum of two overlapping regions in the input samples, 
## up to maximum amount of overlapping regions equal to the number 
## of input samples.

res = cover(exp, 2, ALL())

## The following statement produces an output dataset with a single 
## output sample. The COVER operation considers all areas defined by 
## a minimum of two overlapping regions in the input samples, 
## up to any amount of overlapping regions.

res = cover(exp, 2, ANY())

## The following statement produces an output dataset with a single 
## output sample. The COVER operation considers all areas defined by 
## minimum of overlapping regions in the input samples equal to half of 
## the number of input samples, up to any amount of overlapping regions.

res = cover(exp, ALL()/2, ANY())

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