sfpmean: Pointwise mean survival fractions for curves with several...
In ZytoHMGU/CFAssay: Statistical analysis for the Colony Formation Assay

Description Usage Arguments Details Value Author(s) See Also Examples

The function calculates mean survival fractions for curves averaged over experimental replicates. The function is employed by function plot.cellsurvLQfit for plotting observed means

1	sfpmean(X, S0=NULL)

`X`	A data frame which contains columns `Exp, dose, ncells, ncolonies` and if `S0=NULL`, `X` has to contain a further column `pe` for plating efficiencies.
`S0`	If not `NULL`, a named numerical vector of length equal to the number of different experiments, i.e. `length(S0)==length(unique(X$Exp))` has to be `TRUE`. Default is `S0=NULL`, i.e. undefined.

In the data frame X, Exp identifies the experimental replicates and may be numeric or non-numeric. S0 may contain plating efficiencies for each replicate, resulting from function pes or from cellsurvLQfit (fitted). When S0=NULL, X must have a column with name pe, containing the plating efficiencies.

A numerical matrix with two rows, the first row containing the survival fractions for each radiation dose, second row the standard deviations.

Herbert Braselmann

pes, cellsurvLQfit, plot.cellsurvLQfit

datatab <- read.table(system.file("doc", "expl1_cellsurvcurves.txt", package="CFAssay"), header=TRUE, sep="\t")
X <- subset(datatab, cline=="okf6TERT1")
S0 <- pes(X)$pe  #observed plating efficiencies
length(S0)==length(unique(X$Exp)) #length ok?
names(S0) <- pes(X)$Exp
sfpmean(X, S0)
fit <- cellsurvLQfit(X)
fit$coef  #contains fitted log-pe
grep("Exp",names(fit$coef))
S01 <- exp(fit$coef[1:8])  #fitted pe
sfpmean(X, S01)
## Not run: sfpmean(X)  #yields an error for this data set