pes: Calculation of plating efficiencies from a curve data set...

In CFAssay: Statistical analysis for the Colony Formation Assay

Description

The function calculates plating efficiencies, i.e. fractions of colonies per cell of untreated cells, for every experimental replicate in a data frame with one specified curve. For that, lines with zero dose (dose = 0) are extracted from the data frame.

Usage

pes(X)

Arguments

X	A data frame which contains columns Exp, dose, ncells, ncolonies.

Details

In the data frame X, Exp identifies the experimental replicates and may be numeric or non-numeric.

Value

The function returns a data frame with three columns Exp, pe and S0, containing experiment identifiers (biological replicates), measured plating efficiencies and plating efficiencies fitted separately for each repeated experiments. Rows of the data frame are named for the different experiments.

Author(s)

Herbert Braselmann

Examples

datatab <- read.table(system.file("doc", "expl1_cellsurvcurves.txt", package="CFAssay"), header=TRUE, sep="\t")
X <- subset(datatab, cline=="okf6TERT1")  #Specification of curve
pes(X)
pes(subset(datatab, cline=="cal33") )

Example output

   Exp        pe         S0
e1  e1 0.1900000 0.19435814
e2  e2 0.1433333 0.16709804
e3  e3        NA 0.10614361
e4  e4        NA 0.15587112
e5  e5        NA 0.09512325
e6  e6        NA 0.17026218
e7  e7        NA 0.13032088
e8  e8        NA 0.12187062
   Exp        pe         S0
e1  e1 0.2022222 0.21162383
e2  e2        NA 0.15784332
e3  e3        NA 0.09439330
e4  e4        NA 0.06786303

CFAssay documentation built on Nov. 8, 2020, 11:10 p.m.