analyze_survival: analyze_survival

In CFAcoop: Colony Formation Assay: Taking into Account Cellular Cooperation

Description

wrapper function for robust analysis of 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.

Usage

analyze_survival(RD, name = "no name", xtreat = NULL, C = 20)

Arguments

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	number of colonies counted for which the survival fraction is to be calculated (default = 20))

Value

list object containing several experiments and treatments organized for convenient plotting with plot_sf

Examples

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 = 20)
SF[[2]] <- analyze_survival(RD = df.2,
                            name = "cell line b",
                            xtreat = c(0,1,4))

CFAcoop documentation built on June 11, 2021, 5:14 p.m.