tcplLoadData: Load tcpl data

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

Load tcpl data

Description

tcplLoadData queries the tcpl databases and returns a data.table with data for the given level and data type.

Usage

tcplLoadData(lvl, fld = NULL, val = NULL, type = "mc", add.fld = TRUE)

Arguments

lvl	Integer of length 1, the level of data to load
fld	Character, the field(s) to query on
val	List, vectors of values for each field to query on. Must be in the same order as 'fld'.
type	Character of length 1, the data type, "sc" or "mc"
add.fld	Boolean if true we want to return the additional parameters fit with tcplfit2

Details

The data type can be either 'mc' for mutliple concentration data, or 'sc' for single concentration data. Multiple concentration data will be loaded into the 'mc' tables, whereas the single concentration will be loaded into the 'sc' tables.

Setting 'lvl' to "agg" will return an aggregate table containing the m4id with the concentration-response data and m3id to map back to well-level information.

If tcplConf() was set with "API" as the driver, then tcplLoadData will return data from the CCTE Bioactivity API. API data is available for type = 'mc' and lvl = c(3,4,5,6) and 'agg'. Only fields relating to the requested level are returned, but not all fields that usually return from invitrodb are available from the API. To have all fields available from the API return, regardless of what lvl is set to, set add.fld to TRUE. API query-able fields include "aeid", "spid", "m4id", and "dtxsid".

Leaving fld NULL will return all data.

Valid fld inputs are based on the data level and type:

type	lvl	Queried tables
sc	0	sc0
sc	1	sc0, sc1
sc	agg	sc1, sc2_agg
sc	2	sc2
mc	0	mc0
mc	1	mc0, mc1
mc	2	mc0, mc1, mc2
mc	3	mc0, mc1, mc3
mc	agg	mc3, mc4_agg
mc	4	mc4
mc	5	mc4, mc5
mc	6	mc4, mc6
mc	7	mc4, mc7

Value

A data.table containing data for the given fields.

See Also

tcplQuery, data.table

Examples

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

## Load all of level 0 for multiple-concentration data, note 'mc' is the
## default value for type
tcplLoadData(lvl = 0)

## Load all of level 1 for single-concentration
tcplLoadData(lvl = 1, type = "sc")

## List the fields available for level 1, coming from tables mc0 and mc1
tcplListFlds(tbl = "mc0")
tcplListFlds(tbl = "mc1")

## Load level 0 data where the well type is "t" and the concentration
## index is 3 or 4
tcplLoadData(lvl = 1, fld = c("wllt", "cndx"), val = list("t", c(3:4)))

## Reset configuration
options(conf_store)

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