computeIC50 {PharmacoGx} | 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 |
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
a numeric value for the concentration of the nth precentile viability reduction
Functions
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
PharmacoGx version 2.6.0
Index]