Load assay information {GladiaTOX} | R Documentation

## Functions for loading assay information

### Description

These functions query the gtox databases and returns a data.table with assay ID and name information. More information about the assay hierarchy is available in the overview vignette.

### Usage

    gtoxLoadAcid(fld = NULL, val = NULL, add.fld = NULL)

    gtoxLoadAeid(fld = NULL, val = NULL, add.fld = NULL)

    gtoxLoadAid(fld = NULL, val = NULL, add.fld = NULL)

    gtoxLoadAsid(fld = NULL, val = NULL, add.fld = NULL)

### Arguments

`fld` | Character, the field(s) to query/subset on
`val` | List, vectors of values for each field to query/subset on. Must be in the same order as 'fld'.
`add.fld` | Character, additional field(s) to include, but not query/ subset on

### Details

Each element in the assay hierarchy has its own function, loading the ID and name for the given assay element. For example, `gtoxLoadAsid` will return the assay source ID (asid) and assay source name (asnm).

### Value

A data.table containing the ID, name, and any additional fields.

### Examples

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

    ## The load assay functions can be used without any parameters to list the
    ## full list of registered assay elements:

    ## Assay source ID table
    gtoxLoadAsid()

    ## Assay ID table
    gtoxLoadAid()

    ## Assay component ID table
    gtoxLoadAcid()

    ## Assay endpoint ID table
    gtoxLoadAeid()

    ## Similarly, the user can add fields without doing any element selection:
    gtoxLoadAeid(add.fld = c("asid", "aid", "acid"))

    ## Or, the user can look only at a subset:
    gtoxLoadAeid(fld = "aeid", val = 1, add.fld = "asid")

    ## The field can be any value in one of the corresponding assay element
    ## tables, but the functions also recognize the abbreviated version of
    ## the name fields.
    gtoxListFlds("assay")
    a1 <- gtoxLoadAeid(fld = "anm", val = "Apo Necro (casp37)_4h")
    a2 <- gtoxLoadAeid(fld = "assay_name", val = "Apo Necro (casp37)_4h")
    identical(a1, a2)

    ## Reset configuration
    options(conf_store)

[Package GladiaTOX version 1.10.3 Index]