rgstr_funcs: Functions for registering & updating annotation information
In GladiaTOX: R Package for Processing High Content Screening data

Description Usage Arguments Details Value Examples

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

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gtoxRegister(what, flds)

gtoxUpdate(what, id, flds)

`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

These functions are used to populate the gtox 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 gtox 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
spid (sample): spid, chid
chid (chemical): chid, casn
clib (chemical_library): chid, clib
*vehicle (vehicle): vehicle_name
*waid (assay_plate_well): apid, spid, rowi, coli, wllt, vhid, conc
*apid (assay_plate): aid

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. * indicate PMI-specific fields.

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

## Load current ASID information
gtoxLoadAsid()

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

## Show the newly registered ASID
gtoxLoadAsid(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 gtoxUpdate
i1 <- gtoxLoadAsid()[asnm == "example_asid", asid]
gtoxUpdate(what = "asid", 
id = i1, 
flds = list(assay_source_desc = "example asid description"))
gtoxLoadAsid(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. 
gtoxSendQuery(paste0("DELETE FROM assay_source WHERE asid = ", i1, ";"))

## Reset configuration
options(conf_store)