mthd_funcs: Functions for managing processing methods

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

Functions for managing processing methods

Description

These functions are used to manage which methods are used to process data. They include methods for assigning, clearing, and loading the assigned methods. Also, gtoxMthdList lists the available methods.

Usage

gtoxMthdAssign(lvl, id, mthd_id, ordr = NULL, type)

gtoxMthdClear(lvl, id, mthd_id = NULL, type)

gtoxMthdList(lvl, type = "mc")

gtoxMthdLoad(lvl, id = NULL, type = "mc")

Arguments

lvl	Integer of length 1, the method level
id	Integer, the assay component or assay endpoint id(s)
mthd_id	Integer, the method id(s)
ordr	Integer, the order in which to execute the analysis methods, must be the same length as mthd_id, does not apply to levels 5 or 6
type	Character of length 1, the data type, "sc" or "mc"

Details

gtoxMthdLoad loads the assigned methods for the given level and ID(s). Similarly, gtoxMthdList displays the available methods for the given level. These two functions do not make any changes to the database.

Unlike the -Load and -List functions, the -Assign and -Clear functions alter the database and trigger a delete cascade. gtoxMthdAssign assigns methods to the given ID(s), and gtoxMthdClear removes methods. In addition to the method ID ('mthd_id'), assigning methods at some levels require an order ('ordr'). The 'ordr' parameter is necessary to allow progression of methods at level one for single-concentration processing, and levels two and three for multiple-concentration processing. More information about method assignments and the delete cascade are available in the package vignette.

Value

None

Examples

## Not run: 
## Assign level 2 methods (none for all acid values)
gtoxMthdAssign(lvl = 2L, id = 1L, mthd_id = 1, ordr = 1, type = "mc")

## Process data
gtoxRun(asid = 1L, slvl = 1, elvl = 6, mc.cores = 2)

## End(Not run)


## Not run: 
## Clear level 2 methods
gtoxMthdClear(lvl = 2L, id = 1L, mthd_id = NULL, type = "mc") 

## Assign level 2 methods (none for all acid values)
gtoxMthdAssign(lvl = 2L, id = 1L, mthd_id = 1, ordr = 1, type = "mc")

## Process data
gtoxRun(asid = 1L, slvl = 1, elvl = 6, mc.cores = 2)

## End(Not run)

## Store the current config settings, so they can be reloaded at the end 
## of the examples
conf_store <- gtoxConfList()
gtoxConfDefault()

## gtoxListMthd allows the user to display the available methods for 
## a given level and data type
head(gtoxMthdList(lvl = 2, type = "mc"))

## gtoxLoadMthd shows which methods are assigned for the given ID, level,
## and data type. Here we will show how to register, load, and clear methods
## using an acid not in the example database. Note: There is no check for
## whether an ID exists before assigning/clearing methods. 
gtoxMthdLoad(lvl = 2, id = 1, type = "mc")

## Reset configuration
options(conf_store)

pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.