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Computes the AUC for a Drug Dose Viability Curve

Source: R/computeAUC.R
computeAUC.Rd

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.

Usage

computeAUC(
  concentration,
  viability,
  Hill_fit,
  conc_as_log = FALSE,
  viability_as_pct = TRUE,
  trunc = TRUE,
  area.type = c("Fitted", "Actual"),
  verbose = TRUE
)

Arguments

concentration

numeric is a vector of drug concentrations.

viability

numeric 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.

Value

Numeric AUC value

Examples

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)
#> Warning: Warning: y data exceeds negative control.
#> [1] 3.69127