operator-class: OPERATOR object class constructor

In DEIB-GECO/RGMQL: GenoMetric Query Language for R/Bioconductor

OPERATOR object class constructor

Description

This class constructor is used to create instances of OPERATOR object, to be used in GMQL functions that require operator on value.

Usage

META(value, type = NULL)

NIL(type)

SQRT(value)

Arguments

value	string identifying name of metadata attribute
type	string identifying the type of the attribute value; it must be: INTEGER, DOUBLE or STRING. For NIL() function, only INTEGER and DOUBLE are allowed

Details

• META: It prepares input parameter to be passed to library function meta, performing all the type conversions needed

• SQRT: It prepares input parameter to be passed to library function sqrt, performing all the type conversions needed

• NIL: It prepares input parameter to be passed to library function null, performing all the type conversions needed

Value

Operator 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 folder "DATASET" in the subdirectory "example" 
## of the package "RGMQL" and opens such folder as a GMQL dataset 
## named "exp"

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

## This statement allows to select, in all input samples, all those regions 
## for which the region attribute score has a value which is greater 
## than the metadata attribute value "avg_score" in their sample.

data = filter(exp, r_predicate = score > META("avg_score"), NULL)

## This statement defines new numeric region attributes with "null" value. 
## The syntax for creating a new attribute with null value is 
## attribute_name = NULL(TYPE), where type may be INTEGER or DOUBLE.

out = select(exp, regions_update = list(signal = NIL("INTEGER"), 
    pvalue = NIL("DOUBLE")))

## This statement allows to build an output dataset named 'out' such that 
## all the samples from the input dataset 'exp' are conserved, 
## as well as their region attributes (and their values) 
## and their metadata attributes (and their values). 
## The new metadata attribute 'concSq' is added to all output samples 
## with value correspondent to the mathematical squared root 
## of the pre-existing metadata attribute 'concentration'.

out = select(exp, metadata_update = list(concSq = SQRT("concentration")))

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