tcplLoadChem: Load sample/chemical information

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

Load sample/chemical information

Description

tcplLoadChem queries the tcpl database and returns the chemical information for the given field and values.

Usage

tcplLoadChem(field = NULL, val = NULL, exact = TRUE, include.spid = TRUE)

Arguments

field	Character of length 1, the field to query on
val	Vector of values to subset on
exact	Logical, should chemical names be considered exact?
include.spid	Logical, should spid be included?

Details

The 'field' parameter is named differently from the 'fld' parameter seen in other functions because it only takes one input.

In the MySQL environment the user should be able to give partial chemical name strings, to find chemicals with similar names. For example, setting 'val' to "phenol" when 'field' is "chnm" and 'exact' is FALSE might pull up the chemicals "Bisphenol A" and "4-Butylphenol". More technically, setting 'exact' to FALSE passes the string in 'val' to an RLIKE statement within the MySQL query.

Value

A data.table with the chemical 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 registered chemicals with their
## sample IDs
tcplLoadChem()

## Or the user can exclude spid and get a unique list of chemicals
tcplLoadChem(include.spid = FALSE)

## In addition, the user can retrieve only the registered chemicals from the chemical table
tcplLoadChem(field = 'chem.only')

## Other examples:
tcplLoadChem(field = "chnm", val = "Bisphenol A")
tcplLoadChem(field = "chid", val = 20182)

## Reset configuration
options(conf_store)

USEPA/CompTox-ToxCast-tcpl documentation built on April 22, 2024, 12:37 p.m.