Table 1 R commands for the two presented examples
From: CFAssay: statistical analysis of the colony formation assay
R Command | Comment |
|---|---|
LQ cell survival curves | |
> library(CFAssay) | Loads the package |
> filename <- ~expl1_cellsurvcurves.txt~ | |
> datapath <- system.file(~doc~, filename, package=~CFAssay~) | Gets the path to the example data |
> datatab <- read.table(datapath, header=TRUE, sep=~\t~) | Reads the data |
> X <- subset(datatab, cline==~okf6TERT1~) | Selects OKF6 cell survival data |
> print(cellsurvLQfit(X, method=~ml~)) | Fits LQ model with maximum likelihood |
> print(cellsurvLQfit(X, method=~ls~)) | Fits LQ model with least squares |
> print(cellsurvLQdiff(datatab, curvevar=~cline~)) | Compares curves from two cell lines |
Knockdown and treatment experiment | |
> filename <- ~exp2_2waycfa.txt~ | |
> datapath <- system.file(~doc~, filename, package=~CFAssay~) | Gets the path to the example data |
> datatab <- read.table(datapath, header=TRUE, sep=~\t~) | Reads the data |
> print(cfa2way(datatab, A=~siRNA~, B=~x5fuCis~, param=~A/B~, method=~ml~)) | Fits LQ model with maximum likelihood |
> print(cfa2way(datatab, A=~siRNA~, B=~x5fuCis~, param=~A/B~, method=~ls~)) | Fits LQ model with least squares |