computeAUC: Computes the AUC for a Drug Dose Viability Curve

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Computes the AUC for a Drug Dose Viability Curve

Description

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)

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.