Calculates the Dose Enhancement Ratio — calculateDER • CellSurvAssay

It helps you calculate the Dose Enhancement Ratio automatically without going through any data wrangling steps or calculation.

Usage

calculateDER(data, control, treatment, S, method = "ml", PEmethod = "fit")

Arguments

data: A data frame containing at least the following five columns: "cline", "Exp", "dose", "ncells", "ncolonies".
control: Name of the cell-line/group that will act as control (numerator in the ratio).
treatment: Name of the cell-line/group that will act as treatment (denominator in the ratio).
S: The survival fraction value for which you want to calculate your DER.
method: Method used for the fit. It's "ml" (maximum likelihood) by default. Can be "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

The Dose Enhancement Ratio of Control:Treatment.

Examples

datatab <- CASP8_data
calculateDER(datatab, "shCASP8-NT", "shCASP8-N", 0.25)
#> *** Dose Enhancement Ratio ***
#> 
#> control = shCASP8-NT
#> treatment = shCASP8-N
#> survival fraction = 0.25
#> method = ml
#> PEmethod = fit
#> DER = 0.945622065301553
#> 
#> *** Analysis by CellSurvAssay v0.99.0 ***
calculateDER(datatab, "shCASP8-NT", "shCASP8-N", 0.25, method = "ls", PEmethod = "fix")
#> *** Dose Enhancement Ratio ***
#> 
#> control = shCASP8-NT
#> treatment = shCASP8-N
#> survival fraction = 0.25
#> method = ls
#> PEmethod = fix
#> DER = 0.951520220901901
#> 
#> *** Analysis by CellSurvAssay v0.99.0 ***