rgstr_funcs: Functions for registering & updating annotation information

In tcpl: ToxCast Data Analysis Pipeline

Functions for registering & updating annotation information

Description

These functions are used to register and update the chemical and assay annotation information.

Usage

tcplRegister(what, flds)

tcplUpdate(what, id, flds)

Arguments

what	Character of length 1, the name of the ID to register or update
flds	Named list, the other fields and their values
id	Integer, the ID value(s) to update

Details

These functions are used to populate the tcpl database with the necessary annotation information to complete the processing. As shown in the package vignette, the package requires some information about the samples and assays before data can be loaded into the tcpl database.

Depending on what is being registered, different information is required. The following table lists the fields that can be registered/updated by these functions, and the minimal fields required for registering a new ID. (The database table affected is in parentheses.)

• asid (assay_source): assay_source_name

• aid (assay): asid, assay_name, assay_footprint

• acid (assay_component): aid, assay_component_name

• aeid (assay_component_endpoint): acid, assay_component_endpoint_name, normalized_data_type

• acsn (assay_component_map): acid, acsn

• spid (sample): spid, chid

• chid (chemical): chid, casn

• clib (chemical_library): chid, clib

Note: The functions accept the abbreviated forms of the names, ie. "aenm" rather than the full "assay_component_endpoint_name." More information about the registration process and all of the fields is available in the vignette.

Examples

## Not run: 
## Store the current config settings, so they can be reloaded at the end 
## of the examples
conf_store <- tcplConfList()
tcplConfDefault()

## Load current ASID information
tcplLoadAsid()

## Register a new assay source
tcplRegister(what = "asid", flds = list(asnm = "example_asid"))

## Show the newly registered ASID
tcplLoadAsid(add.fld = "assay_source_desc")

## Notice that the newly created ASID does not have an assay_source_desc.
## The field could have been defined during the registration process, but
## can also be updated using tcplUpdate
i1 <- tcplLoadAsid()[asnm == "example_asid", asid]
tcplUpdate(what = "asid", 
           id = i1, 
           flds = list(assay_source_desc = "example asid description"))
tcplLoadAsid(add.fld = "assay_source_desc")

## Remove the created ASID. Note: Manually deleting primary keys can cause
## serious database problems and should not generally be done. 

## If using the tcplLite DRVR, must specify table name
if (conf_store$TCPL_DRVR == 'MySQL') {
  tcplSendQuery(paste0("DELETE FROM assay_source WHERE asid = ", i1, ";"))
} else {
  qy <- paste0("SELECT * FROM assay_source WHERE NOT asid = ", i1, ";")
  tcplSendQuery(qy, tbl='assay_source', delete=TRUE)
}

## Reset configuration
options(conf_store)

## End(Not run)

tcpl documentation built on Oct. 7, 2023, 1:06 a.m.