MC6_Methods: Load list of level 6 multiple-concentration flag methods

In tcpl: ToxCast Data Analysis Pipeline

Load list of level 6 multiple-concentration flag methods

Description

mc6_mthds returns a list of flag methods to be used during level 6 multiple-concentration processing.

Usage

mc6_mthds()

Value

A list functions

Available Methods

More information about the level 6 multiple-concentration processing is available in the package vignette, "Data_processing."

modl.directionality.fail

Flag series if model directionality is questionable, i.e. if the winning model direction was opposite, more responses (resp) would have exceeded the cutoff (coff). If loss was winning directionality (top < 0), flag if count(resp<-1*coff)<2*count(resp>coff). If gain was winning directionality (top > 0), flag if count(resp>coff)<2*count(resp<-1*coff).

low.nrep

Flag series if the average number of replicates per concentration is less than 2; nrep < 2.

low.nconc

Flag series if 4 concentrations or less were tested; nconc<=4.

bmd.high

Flag series if modeled benchmark dose (BMD) is greater than AC50 (concentration at 50 percent maximal response). This is indicates high variability in baseline response in excess of more than half of the maximal response.

singlept.hit.high

Flag single-point hit that's only at the highest conc tested, where series is an active hit call (hitc >= 0.9) with the median response observed above baseline occurring only at the highest tested concentration tested.

singlept.hit.mid

Flag single-point hit that's not at the highest conc tested, where series is an active hit call (hitc >= 0.9) with the median response observed above baseline occurring only at one concentration and not the highest concentration tested.

multipoint.neg

Flag multi-point miss, where series is an inactive hit call (hitc < 0.9) with multiple median responses observed above baseline.

gnls.lowconc

Flag series where winning model is gain-loss (gnls) and the gain AC50 is less than the minimum tested concentration, and the loss AC50 is less than the mean tested concentration.

noise

Flag series as noisy if the quality of fit as calculated by the root mean square error (rmse) for the series is greater than the cutoff (coff); rmse > coff.

border

Flag series if borderline activity is suspected based on modeled top parameter (top) relative to cutoff (coff); |top|<=1.2*coff~or~|top|>=0.8*coff.

overfit.hit

Method not yet updated for tcpl implementation. Flag hit-calls that would get changed after doing the small N correction to the aic values.

efficacy.50

Flag low efficacy hits if series has an active hit call (hitc >= 0.9) and efficacy values (e.g. top and maximum median response) less than 50 percent; intended for biochemical assays. If hitc>=0.9 and coff>=5, then flag when top<50 or maxmed < 50. If hitc>=0.9 and coff<5, then flag when top<\log_{2}{1.5} or maxmed<\log_{2}{1.5}.

ac50.lowconc

Flag series with an active hit call (hitc >= 0.9) if AC50 (concentration at 50 percent maximal response) is less than the lowest concentration tested; if hitc>=0.9 and ac50<10^{log_{c}{min}}, then flag.

viability.gnls

Flag series with an active hit call (hitc >= 0.9) if denoted as cell viability assay with winning model is gain-loss (gnls); if hitc >= 0.9, modl = "gnls" and cell_viability_assay = 1, then flag.

no.med.gt.3bmad

Flag series where no median response values are greater than baseline as defined by 3 times the baseline median absolute deviation (bmad); nmed_gtbl = 0, where nmed_gtbl is the number of medians greater than 3 * bmad.

Note

This function is not exported and is not intended to be used by the user.

See Also

mc6, Method functions to query what methods get applied to each aeid.

tcpl documentation built on Oct. 7, 2023, 1:06 a.m.