computeIC50 {ToxicoGx} | R Documentation

## 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` | [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.

### Value

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)

[Package ToxicoGx version 1.0.1 Index]