sumIC50: Summarise drug effect across concentrations using a...

In lujunyan1118/DrugScreenExplorer_dev: A pipeline for processing drug sensitivity screen data

Description

This function will fit a 4-parameter log-logistic model using dr4pl package based on the input dose-response table and return the model parameters as well as integrated area under the fitted sigmoid curve.

Usage

sumIC50(formula, data = NULL, minConc = 0, maxConc = 15, n = 100, ...)

Arguments

formula	formula for the curve fitting.
data	a data frame containing the raw concentration and the viability value.
minConc	lower bound of concentrations for the integration of area under curve, default value is 0.
maxConc	upper bound of concentrations for the integration of area under curve, default value is 15.
n	number of bins for integration.
...	further arguments to be passed to dr4pl function.

Value

a dataframe with only one row and four columns:

UpperLimit	the upper limit of the fitted logistic model
IC50	the half maximal inhibitory concentration (IC50), or the half maximal effective concentration (EC50), depends on the type of input data
Slope	the slope of the fitted logistic model
lowerLimit	the upper limit of the fitted logistic model
AUC	the area under the fitted sigmoid doese-response curve

If the model fitting is failed, all values in the dataframe will be NA.

Examples

# create an example dose-response table
doseTab <- data.frame(viability = c(1.0, 0.95, 0.5, 0.2, 0.1),
                      concentration = c(0.001, 0.01, 0.1, 1, 10))

# get the parameters
sumIC50(viability ~ concentration, data = doseTab)

lujunyan1118/DrugScreenExplorer_dev documentation built on Dec. 21, 2021, 12:42 p.m.