MC6_Methods: Load list of level 6 multiple-concentration flag methods
In daynefiler/tcpl: ToxCast Data Analysis Pipeline

Description Usage Value Available Methods See Also

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

1	mc6_mthds()

A list functions

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

singlept.hit.high: The singlept.hit.high flag identifies concentration series where the median response was greater than 3*bmad only at the highest tested concentration and the series had an active hit-call.
singlept.hit.mid: The singlept.hit.mid flag identifies concentration series where the median response was greater than 3*bmad at only one concentration (not the highest tested concentration) and the series had an active hit-call.
multipoint.neg: The multipoint.neg flag identifies concentration series with response medians greater than 3*bmad at multiple concentrations and an inactive hit-call.
gnls.lowconc: The gnls.lowconc flag identifies concentration series where the gain-loss model won, the gain AC50 is less than the minimum tested concentration, and the loss AC50 is less than the mean tested concentration.
noise: The noise flag attempts to identify noisy concentration series by flagging series where the root mean square error for the series is greater than the cutoff for the assay endpoint.
border.hit: The border.hit flag identifies active concentration series where the top parameter of the winning model was less than or equal to 1.2*cut-off or the the activity probablity was less than 0.9.
border.miss: The border.miss flag identifies inactive concentration series where either the Hill or gain-loss top parameter was greater than or equal to 0.8*cut-off and the activity probability was greater than 0.5.
overfit.hit: The overfit.hit flag recalculates the model winner after applying a small sample correction factor to the AIC values. If the hit-call would be changed after applying the small sample correction factor the series is flagged. Series with less than 5 concentrations where the hill model won and series with less than 7 concentrations where the gain-loss model won are automatically flagged.
efficacy.50: The efficacy.50 flag identifies concentration series with efficacy values (either the modeled top parameter for the winning model or the maximum median response) are less than 50 for percent activity data or log2(1.5) for fold induction data
modlga.lowconc: The modlga.lowconc flag identifies concentration series with modl_ga (AC50) values less than the minimum tested concentration.