Bioconductor

filter

R Documentation

Method filter

Description

Wrapper to GMQL SELECT operator

It creates a new dataset from an existing one by extracting a subset of samples and/or regions from the input dataset according to the predicate. Each sample in the output dataset has the same region attributes, values, and metadata as in the input dataset. When semijoin function is defined, it extracts those samples containing all metadata attributes defined in semijoin clause with at least one metadata value in common with semijoin dataset. If no metadata in common between input dataset and semijoin dataset, no sample is extracted.

Usage

## S4 method for signature 'GMQLDataset'
filter(
  .data,
  m_predicate = NULL,
  r_predicate = NULL,
  semijoin = NULL,
  .by = NULL,
  .preserve = NULL
)

Arguments

`.data`	GMQLDataset class object
`m_predicate`	logical predicate made up by R logical operations on metadata attributes. Only !, \|, \|\|, &, && are admitted.
`r_predicate`	logical predicate made up by R logical operations on region attributes. Only !, \|, \|\|, &, && are admitted.
`semijoin`	`semijoin` function to define filter method with semijoin condition (see examples).
`.by`	parameters inherited, unused with GMQLDateset data object
`.preserve`	parameters inherited, unused with GMQLDateset data 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 folder "DATASET" in the subdirectory "example" 
## of the package "RGMQL" and opens such folder as a GMQL dataset 
## named "data"

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

## This statement selects from input the data samples of patients younger 
## than 70 years old, based on filtering on sample metadata attribute 
## 'patient_age'

filter_data <- filter(data, patient_age < 70, NULL)

## This statement defines the path to the folder "DATASET_GDM" in the 
## subdirectory "example" of the package "RGMQL" and opens such folder 
## as a GMQL dataset named "join_data"

test_path2 <- system.file("example", "DATASET_GDM", package = "RGMQL")
join_data <- read_gmql(test_path2) 

## This statement creates a new dataset called 'jun_tf' by selecting those 
## samples and their regions from the existing 'data' dataset such that:
## Each output sample has a metadata attribute called antibody_target 
## with value JUN.
## Each output sample also has not a metadata attribute called "cell" 
## that has the same value of at least one of the values that a metadata 
## attribute equally called cell has in at least one sample 
## of the 'join_data' dataset.
## For each sample satisfying previous conditions, only its regions that 
## have a region attribute called 'pvalue' with the associated value 
## less than 0.01 are conserved in output

jun_tf <- filter(data, antibody_target == "JUN", pvalue < 0.01, 
    semijoin(join_data, FALSE, conds("cell")))

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