
Remove endpoints with specific data quality flags from data
Source:R/get_chemical_summary.R
remove_flags.Rd
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".