computeAUC {ToxicoGx} | R Documentation |
Returns the AUC (Area Under the drug response Curve) given concentration and viability as input, normalized by the concentration range of the experiment. The area returned is the response (1-Viablility) area, i.e. area under the curve when the response curve is plotted on a log10 concentration scale, with high AUC implying high sensitivity to the drug. The function can calculate both the area under a fitted Hill Curve to the data, and a trapz numeric integral of the actual data provided. Alternatively, the parameters of a Hill Slope returned by logLogisticRegression can be passed in if they already known.
computeAUC( concentration, viability, Hill_fit, conc_as_log = FALSE, viability_as_pct = TRUE, trunc = TRUE, area.type = c("Fitted", "Actual"), verbose = TRUE )
concentration |
[vector] is a vector of drug concentrations. |
viability |
[vector] is a vector whose entries are the viability values observed in the presence of the drug concentrations whose logarithms are in the corresponding entries of conc, where viability 0 indicates that all cells died, and viability 1 indicates that the drug had no effect on the cells. |
Hill_fit |
[list or vector] In the order: c("Hill Slope", "E_inf", "EC50"), the parameters of a Hill Slope as returned by logLogisticRegression. If conc_as_log is set then the function assumes logEC50 is passed in, and if viability_as_pct flag is set, it assumes E_inf is passed in as a percent. Otherwise, E_inf is assumed to be a decimal, and EC50 as a concentration. |
conc_as_log |
[logical], if true, assumes that log10-concentration data has been given rather than concentration data. |
viability_as_pct |
[logical], if false, assumes that viability is given as a decimal rather than a percentage, and returns AUC as a decimal. Otherwise, viability is interpreted as percent, and AUC is returned 0-100. |
trunc |
[logical], if true, causes viability data to be truncated to lie between 0 and 1 before curve-fitting is performed. |
area.type |
Should the area be computed using the actual data ("Actual"), or a fitted curve ("Fitted") |
verbose |
[logical], if true, causes warnings thrown by the function to be printed. |
Numeric AUC value
dose <- c("0.0025","0.008","0.025","0.08","0.25","0.8","2.53","8") viability <- c("108.67","111","102.16","100.27","90","87","74","57") computeAUC(dose, viability)