toxEval (version 1.4.0)

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_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)