lqmodelFit: Fits the Linear Quadratic Model

In PickeringLab/CellSurvAssay: Clonogenic Survival Analysis in R made easy!

Fits the Linear Quadratic Model

Description

It helps fit the linear quadratic model using the cellsurvLQfit function of the CFAssay package, but automates the data wrangling steps, thus making it more convenient to use for beginner R users. Visit https://bioconductor.org/packages/release/bioc/html/CFAssay.html for more details about the method of the fit.

Usage

lqmodelFit(data, ctype, method = "ml", PEmethod = "fit")

Arguments

data	A data frame containing at least the following five columns with these exact names: "cline", "Exp", "dose", "ncells", "ncolonies".
ctype	Name of the cell-line/group for which the model is to be fit.
method	Method used for the fit. It's "ml" (maximum likelihood) by default. Also accepts "ls" (least squares) or "franken" (weighted least squares as described by Franken eta al.(2006)).
PEmethod	Controls the value of the plating efficiencies. "fit" calculates fitted plating efficiencies as model parameters, "fix" uses fixed ones calculated from the observed zero dose data.

Value

An object of class cellsurvLQfit, as returned by cellsurvLQfit.

Examples

datatab <- CASP8_data
lqmodelFit(datatab, "control-B")
lqmodelFit(datatab, "control-B", method = "ls", PEmethod = "fix")

PickeringLab/CellSurvAssay documentation built on June 15, 2022, 12:33 a.m.