toxEval (version 1.0.3)

remove_flags: 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*

Asterisks indicate flags removed in the function as default.

Usage

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

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".

Examples

# NOT RUN {
CAS <- c("121-00-6","136-85-6","80-05-7","84-65-1","5436-43-1","126-73-8")
ACC <- get_ACC(CAS)
ACC <- remove_flags(ACC)
# }