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

Description Usage Arguments Value Functions Examples

View source: R/computeICn.R

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

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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

Examples

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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)

ToxicoGx documentation built on Nov. 19, 2020, 2 a.m.