gtoxPrepOtpt: Map assay/chemcial ID values to annotation information

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

Map assay/chemcial ID values to annotation information

Description

gtoxPrepOtpt queries the chemical and assay information from the gtox database, and maps the annotation information to the given data.

Usage

gtoxPrepOtpt(dat, ids = NULL)

Arguments

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

Details

gtoxPrepOtpt 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 <- gtoxConfList()
gtoxConfDefault()

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

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

## Map chemical annotation only
d2 <- gtoxPrepOtpt(d1, ids = "spid")
"chnm" %in% names(d2) ## TRUE
"acnm" %in% names(d2) ## FALSE

## Map all annotations
d3 <- gtoxPrepOtpt(d1) ## Also works if function is given d2
"chnm" %in% names(d2) ## TRUE
"acnm" %in% names(d2) ## FALSE

## Reset configuration
options(conf_store)

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