tcplPrepOtpt: Map assay/chemical ID values to annotation information

In USEPA/CompTox-ToxCast-tcpl: ToxCast Data Analysis Pipeline

Map assay/chemical ID values to annotation information

Description

tcplPrepOtpt queries the chemical and assay information from the tcpl database, and maps the annotation information to the given data.

Usage

tcplPrepOtpt(dat, ids = NULL)

Arguments

dat	data.table, output from tcplLoadData
ids	Character, (optional) a subset of ID fields to map

Details

tcplPrepOtpt is used to map chemical and assay identifiers to their respective names and annotation information to create a human-readable table that is more suitable for an export/output.

By default the function will map sample ID (spid), assay component id (acid), and assay endpoint ID (aeid) values. However, if 'ids' is not null, the function will only attempt to map the ID fields given by 'ids.'

Value

The given data.table with chemical and assay information mapped

Examples

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

## Load some example data
d1 <- tcplLoadData(1)

## Check for chemical name in 'dat'
"chnm" %in% names(d1) ## FALSE

#' ## Map all annotations 
d2 <- tcplPrepOtpt(d1) ##
"chnm" %in% names(d2) ## TRUE
"acnm" %in% names(d2) ## TRUE
 
## Map chemical annotation only
d3 <- tcplPrepOtpt(d1, ids = "spid")
"chnm" %in% names(d3) ## TRUE
"acnm" %in% names(d3) ## FALSE

## Reset configuration
options(conf_store)

USEPA/CompTox-ToxCast-tcpl documentation built on April 22, 2024, 12:37 p.m.