mthd_funcs: Functions for managing processing methods

In tcpl: ToxCast Data Analysis Pipeline

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, tcplMthdList lists the available methods.

Usage

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

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

tcplMthdList(lvl, type = "mc")

tcplMthdLoad(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

tcplMthdLoad loads the assigned methods for the given level and ID(s). Similarly, tcplMthdList 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. tcplMthdAssign assigns methods to the given ID(s), and tcplMthdClear 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.

Examples

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

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

## tcplLoadMthd 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. 
tcplMthdLoad(lvl = 2, id = 55, type = "mc")

## Not run: 
## ACID 55 does not have any methods. Assign methods from the list above. 
tcplMthdAssign(lvl = 2, 
               id = 55, 
               mthd_id = c(3, 4, 2), 
               ordr = 1:3, 
               type = "mc")
## Method assignment can be done for multiple assays, too. 
tcplMthdAssign(lvl = 2, 
               id = 53:54, 
               mthd_id = c(3, 4, 2), 
               ordr = 1:3, 
               type = "mc")
               
## Cleanup example method assigments
tcplMthdClear(lvl = 2, id = 53:55, type = "mc")

## End(Not run)
## Reset configuration
options(conf_store)

tcpl documentation built on Oct. 7, 2023, 1:06 a.m.