computeICn: Computes the ICn for any n in 0-100 for a Drug Dose Viability...
In PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Description Usage Arguments Value Functions Examples

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.

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
)

`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, 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.

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

computeIC50: Returns the IC50 of a Drug Dose response curve

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)