computeICn: Computes the ICn for any n in 0-100 for a Drug Dose Viability...

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

Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve

Description

Returns the ICn for any given nth percentile when given concentration and viability as input, normalized by the concentration range of the experiment. A Hill Slope is first fit to the data, and the ICn is inferred from the fitted curve. Alternatively, the parameters of a Hill Slope returned by logLogisticRegression can be passed in if they already known.

Usage

computeIC50(
  concentration,
  viability,
  Hill_fit,
  conc_as_log = FALSE,
  viability_as_pct = TRUE,
  verbose = TRUE,
  trunc = TRUE
)

computeICn(
  concentration,
  viability,
  Hill_fit,
  n,
  conc_as_log = FALSE,
  viability_as_pct = TRUE,
  verbose = TRUE,
  trunc = 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, and that log10(ICn) should be returned instead of ICn.
viability_as_pct	logical, if false, assumes that viability is given as a decimal rather than a percentage, and that E_inf passed in as decimal.
verbose	logical, if true, causes warnings thrown by the function to be printed.
trunc	logical, if true, causes viability data to be truncated to lie between 0 and 1 before curve-fitting is performed.
n	numeric The percentile concentration to compute. If viability_as_pct set, assumed to be percentage, otherwise assumed to be a decimal value.

Value

numeric(1) The ICn of the Hill curve over the specified dose range.

a numeric value for the concentration of the nth precentile viability reduction

Functions

• computeIC50(): Returns the IC50 of a Drug Dose response curve

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)
computeIC50(dose, viability)
computeICn(dose, viability, n=10)

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