analyze_survival {CFAcoop} | R Documentation |
wrapper function for robust analysis clonogenic survival data from the colony formation assay according to Brix et al. (2020), Radiation Oncology. Mean values are calculated and used for power regression. Resulting coefficients are used for calculation of survival fractions and corresponding uncertainty analysis.
analyze_survival(RD, name = "no name", xtreat = NULL, c_range = c(5, 20, 100))
RD |
data.frame or matrix containing a table of experiment data |
name |
optional: experiment name (e.g. name of cell line) |
xtreat |
optional: treatment dose of the colonies counted in the corresponding columns of RD |
c_range |
number or vector of numbers of colonies counted for which the survival fraction is to be calculated (default = c(5, 20, 100)) |
list object containing several experiments and treatments organized
for convenient plotting with plot_sf
seeded <- rep(10^(seq(1,5,0.5)),each = 3) df.1 <- data.frame( "seeded" = seeded, "counted1" = 0.4 * seeded^1.1 * rnorm(n = length(seeded),1,0.05), "counted2" = 0.2 * seeded^1.125 * rnorm(n = length(seeded),1,0.05), "counted3" = 0.05 * seeded^1.25 * rnorm(n = length(seeded),1,0.05)) df.2 <- data.frame("seeded" = seeded, "counted1" = 0.5 * seeded^1.01 * rnorm(n = length(seeded),1,0.05), "counted2" = 0.4 * seeded^1.0125 * rnorm(n = length(seeded),1,0.05), "counted3" = 0.2 * seeded^1.025 * rnorm(n = length(seeded),1,0.05)) SF <- vector("list",2) SF[[1]] <- analyze_survival(RD = df.1, name = "cell line a", xtreat = c(0,1,4), c_range = c(5,20,100)) SF[[2]] <- analyze_survival(RD = df.2, name = "cell line b", xtreat = c(0,1,4))