Bioconductor

arrange

R Documentation

Method arrange

Description

Wrapper to GMQL ORDER operator

It is used to order either samples or sample regions or both, according to a set of metadata and/or region attributes. Order can be specified as ascending / descending for every attribute. The number of samples and their regions remain the same (unless fetching options are specified), as well as their attributes, but a new ordering metadata and/or region attribute is added. Sorted samples or regions have a new attribute "_order", added to their metadata, or "order" added to their regions, or to both of them as specified in input.

Usage

## S4 method for signature 'GMQLDataset'
arrange(
  .data,
  metadata_ordering = NULL,
  regions_ordering = NULL,
  fetch_opt = "",
  num_fetch = 0L,
  reg_fetch_opt = "",
  reg_num_fetch = 0L,
  .by_group = NULL
)

Arguments

`.data`	GMQLDataset class object
`metadata_ordering`	list of ordering functions containing name of metadata attribute. The functions available are: `ASC`, `DESC`. If NULL, fetch_opt and num_fetch are not considered
`regions_ordering`	list of ordering functions containing name of region attribute. The functions available are: `ASC`, `DESC`. If NULL, reg_fetch_opt and reg_num_fetch are not considered
`fetch_opt`	string indicating the option used to fetch the first k samples; it can assume the values: mtop: it fetches the first k samples mtopp: it fetches the first k percentage of samples. mtopg: it fetches the first k samples in each group. if NULL, num_fetch is not considered
`num_fetch`	integer value identifying the number of samples to fetch; by default it is 0, that means all samples are fetched
`reg_fetch_opt`	string indicating the option used to fetch the first k regions; it can assume the values: rtop: it fetches the first k regions. rtopp: it fetches the first k percentage of regions. rtopg: it fetches the first k regions in each group. if NULL, reg_num_fetch is not considered
`reg_num_fetch`	integer value identifying the number of regions to fetch; by default it is 0, that means all regions are fetched
`.by_group`	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 file as a GMQL dataset named 
## "data" using CustomParser

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

## The following statement orders the samples according to the Region_Count 
## metadata attribute and takes the two samples that have the highest count. 

o = arrange(data, list(ASC("Region_Count")), fetch_opt = "mtop", 
    num_fetch = 2)

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