tcplLoadClib: Load chemical library information

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

Load chemical library information

Description

tcplLoadClib queries the tcpl databases and returns information about the chemical library.

Usage

tcplLoadClib(field = NULL, val = NULL)

Arguments

field	Character of length 1, 'chid' or 'clib', whether to search by chemical id (chid), or chemical library (clib)
val	The values to query on

Details

Chemicals are stored in different libraries by chemical ID. Therefore, it is not possible to delineate samples with the same chemical ID into two distinct chemical libraries. However, it is possible for a chemical ID to belong to more than one (or no) chemical libraries.

When chemicals belong to more than one library, the chemical is listed multiple times (one for each distinct library).

Value

A data.table with the chemical library information for the given parameters.

Examples

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

## Passing no parameters gives all of the chemical ISs that have a chemical
## library registered
clib <- tcplLoadClib()

## Notice there are more rows in tcplLoadClib than in tcplLoadChem, 
## indicating some chemicals must belong to more than library.
chem <- tcplLoadChem(include.spid = FALSE)
nrow(chem)
nrow(clib)

## It is possible that some chemicals do not have a chemical library 
## registered, although this is not the case in the example data.
all(chem$chid %in% clib$chid)

## Show the unique chemical libraries
clib[ , unique(clib)]

## Specifying a chemical library will not show what other libraries a 
## chemical might belong to.
tcplLoadClib(field = "clib", val = "TOXCAST")
tcplLoadClib(field = "chid", val = 20182)

## Reset configuration
options(conf_store)

USEPA/CompTox-ToxCast-tcpl documentation built on April 17, 2024, 6:32 a.m.