This function calculates the linear coefficient alpha and the coefficient beta of the dose-squared term (see manual for this R-package) for colony counts measured for a set of irradiation doses and repeated experiments. The function is a wrapper for the R-functions
lm, which simplifies use of these functions for cell survival data.
cellsurvLQfit(X, method="ml", PEmethod="fit")
A data frame which contains at least columns
Determines the method used for the fit.
Controls the value of the plating efficiencies, i.e. the colony counts for untreated cells.
In the data frame
Exp identifies the experimental replicates and may be numeric or non-numeric.
method="ml" uses R function
glm with quasipoisson family and link function
method="ls" uses R function
PEmethod="fit" fits plating efficiencies for every experiments.
PEmethod="fix" uses observed plating efficiencies. If there is no 0-value in the
PEmethod is overwritten with
X has to contain a further column
pe containing the plating efficiencies, i.e.
ncolonies/ncells from untreated cells, not per hundred or percent.
The function returns an object of class
cellsurvLQfit, which is similar to classes
lm, however containing two additional entries,
PEmethod, which are used for printing and plotting. The full result is returned invisibly, i.e. the function has to be used with
plot or assigned to a variable, say for e.g.
fit as in the example below.
Franken NAP, Rodermond HM, Stap J, et al. Clonogenic assay of cells in vitro. Nature Protoc 2006;1:2315-19.
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datatab<- read.table(system.file("doc", "expl1_cellsurvcurves.txt", package="CFAssay"), header=TRUE, sep="\t") X<- subset(datatab, cline=="okf6TERT1") fit<- cellsurvLQfit(X) #using default options print(fit) print(fit$type) print(fit$PEmethod) #Using other options: print(cellsurvLQfit(X, method="ls")) print(cellsurvLQfit(X, PEmethod="fix")) print(cellsurvLQfit(X, method="ls", PEmethod="fix")) print(cellsurvLQfit(X, method="franken"))
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