gtoxPrepOtpt {GladiaTOX} | R Documentation

## 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)

[Package GladiaTOX version 1.6.1 Index]