sfpmean {CFAssay}R Documentation

Pointwise mean survival fractions for curves with several experimental replicates

Description

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

Usage

sfpmean(X, S0=NULL)

Arguments

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.

Details

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.

Value

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

Author(s)

Herbert Braselmann

See Also

pes, cellsurvLQfit, plot.cellsurvLQfit

Examples

datatab <- read.table(system.file("doc", "expl1_cellsurvcurves.txt", package="CFAssay"), header=TRUE, sep="\t")
X <- subset(datatab, cline=="okf6TERT1")
## S0 from data with fucntion pes
S0 <- pes(X)$pe  #observed plating efficiencies
length(S0)==length(unique(X$Exp)) #length ok?
names(S0) <- pes(X)$Exp
sfpmean(X, S0)
## Not run: 
## S0 from LQ model fit
fit <- cellsurvLQfit(X)
fit$coef  #contains fitted log-pe
grep("Exp",names(fit$coef))
S01 <- exp(fit$coef[1:8])  #fitted pe
sfpmean(X, S01) #names of S01 still to adjust!

## End(Not run)
## Not run: sfpmean(X)  #yields an error for this data set
[Package CFAssay version 1.21.2 Index]