remove_flags: Remove endpoints with specific data quality flags from data

In toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

Remove endpoints with specific data quality flags from data

Description

Through the ToxCast program quality assurance procedures, information is examined and at times, it is necessary to assign a data quality flag to a specific chemical/assay result. A toxEval user may want to include or exclude assay results with certain flags depending on the objectives of a given study. Assay results with specific data quality flags assigned to them can be removed based on their designated flag with the remove_flags function. The flags included in ToxCast, and the associated flagsShort value (used in the remove_flags function) are as follows:

Flag	flagsShort
Borderline active*	Borderline*
Only highest conc above baseline, active*	OnlyHighest*
Only one conc above baseline, active	OneAbove
Noisy data	Noisy
Hit-call potentially confounded by overfitting	HitCall
Gain AC50 < lowest conc & loss AC50 < mean conc*	GainAC50*
Biochemical assay with < 50% efficacy*	Biochemical*
Less than 50% efficacy	LessThan50
AC50 less than lowest concentration tested*	ACCLessThan*
GNLSmodel	GNLSmodel

Asterisks indicate flags removed in the function as default.

Usage

remove_flags(
  ACC,
  flagsShort = c("Borderline", "OnlyHighest", "GainAC50", "Biochemical", "ACCLessThan")
)

Arguments

ACC	data frame with columns: casn, chnm, endPoint, and ACC_value
flagsShort	vector of flags to to trigger REMOVAL of chemical:endPoint combination. Possible values are "Borderline", "OnlyHighest", "OneAbove", "Noisy", "HitCall", "GainAC50", "Biochemical","LessThan50","ACCLessThan","GNLSmodel".

Examples

CAS <- c("121-00-6", "136-85-6", "80-05-7", "84-65-1", "5436-43-1", "126-73-8")
ACC <- get_ACC(CAS)
nrow(ACC)
ACC <- remove_flags(ACC)
nrow(ACC)

toxEval documentation built on April 15, 2023, 1:13 a.m.