assay_funcs: Functions for loading assay information

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

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)

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