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_id	Full Name
5*	Model directionality questionable
6*	Only highest conc above baseline, active
7	Only one conc above baseline, active
8	Multiple points above baseline, inactive
9	Bmd > ac50, indication of high baseline variability
10	Noisy data
11*	Borderline
15*	Gain AC50 < lowest conc & loss AC50 < mean conc
17	Less than 50% efficacy
18*	AC50 less than lowest concentration tested
13	Average number of replicates per conc is less than 2
14	Number of concentrations tested is less than 4
19	Cell viability assay fit with gnls winning model

Asterisks indicate flags removed in the function as default.

Usage

remove_flags(ACC, flag_id = c(5, 6, 11, 15, 18))

Arguments

ACC	data frame with columns: casn, chnm, endPoint, and ACC_value
flag_id	vector of flags to to trigger REMOVAL

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)

# See available flags and associated ids:

flags

ACC <- remove_flags(ACC)
nrow(ACC)

toxEval documentation built on April 12, 2025, 9:12 a.m.