computeABC: Fits dose-response curves to data given by the user and...

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

Fits dose-response curves to data given by the user and returns the ABC of the fitted curves.

Description

Fits dose-response curves to data given by the user and returns the ABC of the fitted curves.

Usage

computeABC(
  conc1,
  conc2,
  viability1,
  viability2,
  Hill_fit1,
  Hill_fit2,
  conc_as_log = FALSE,
  viability_as_pct = TRUE,
  trunc = TRUE,
  verbose = TRUE
)

Arguments

conc1	numeric is a vector of drug concentrations.
conc2	numeric is a vector of drug concentrations.
viability1	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 conc1, expressed as percentages of viability in the absence of any drug.
viability2	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 conc2, expressed as percentages of viability in the absence of any drug.
Hill_fit1	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.
Hill_fit2	lis 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 ABC 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.
verbose	logical, if true, causes warnings thrown by the function to be printed.

Value

The numeric area of the absolute difference between the two hill slopes

Author(s)

Mark Freeman

Examples

dose1 <- c(0.0025,0.008,0.025,0.08,0.25,0.8,2.53,8)
viability1 <- c(108.67,111,102.16,100.27,90,87,74,57)
dose2 <- c(0.0025,0.008,0.025,0.08,0.25,0.8,2.53,8)
viability2 <- c(100.94,112.5,86,104.16,75,68,48,29)
computeABC(dose1, dose2, viability1, viability2)

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