fitIC50: Use the dr4pl package to perform IC50 curve fitting. Can be...

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

Description

Use the dr4pl package to perform IC50 curve fitting. Can be directly used for geom_smooth() in ggplot2.

Usage

fitIC50(formula, data = NULL, weights = NULL, logDose = NULL, ...)

Arguments

formula	formula for the curve fitting.
data	a data frame that contains the concentration values and the normalized viability values or percent inhibition values.
weights	not used, mainly for geom_smooth() purpose
logDose	a numeric value specifying the base of log transformation for concentration, if the concentration is log transformed. The default value is NULL (not log transformed).
...	further arguments to be passed to dr4pl function

Value

fitIC50 returns an object of class 'fitIC50', which is a list containing the following components:

model	the input dose-response table
formula	the formula used for the model fitting
parm_fit	the fitted parameters for a 4-paramater logistic model
logDose	a numeric value specifying the base of log transformation for concentration, if the concentration is log transformed. The default value is NULL (not log transformed).

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))

# fit a four-parameter logistic model using dr4pl package
fitIC50(viability ~ concentration, data = doseTab)

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