data-raw/DATASET.R

In mauromiguelm/tdsR: Growth Response Delay (GRD) of cancer cell lines exposed to drugs

# #test data script -------------------------------------------------------

#define params

k = 0.3
t_ttm <- 1
nreps <- 5
time <- seq(0,3,0.1)
conc <- matrix(base::rep(c(0,seq(0.5,8,length.out = 6)),  each = nreps), dimnames = list(NULL, "concentration"))

params <- matrix(data = c(runif(nreps, min = 2, max = 2), seq(1,1.8,length.out = 5),rep(k,5)), dimnames = list(NULL, c("halfeff", "t_onset","k")), nrow = nreps, ncol = 3)
params <- cbind(do.call("rbind", rep(list(params), 7)), conc)
params <- do.call(rbind, replicate(length(time), params, simplify=FALSE)) #replicate matrix to acommodate time
params <- cbind(params, time = rep(time, times = nreps))

#generate simulated data

sapply(1:dim(params)[1], function(x)

  model_growth(cell_tz = 5, t = params[x,'time'], t_onset = params[x,"t_onset"], k =  params[x,"k"], maxeff = 1.0, halfeff = params[x,"halfeff"], conc = params[x,"concentration"], hill = 1.6)

) -> sample_data

sample_data <- cbind(params, output = sample_data)

sample_data <- reshape2::dcast(data.frame(sample_data),halfeff + k +t_onset +concentration ~time, value.var="output")

# prepare data for input in GRDR

tidyr::gather(data.frame(sample_data, check.names = F), key = "time", value = "cell_count", -c("halfeff","k", "t_onset", "concentration")) -> sample_data

sample_data <- cbind(data.frame(perturbation = paste(sample_data$halfeff,sample_data$k, sample_data$t_onset, sep = "_")), sample_data)

sample_data$perturbation <- factor(sample_data$perturbation,labels = LETTERS[1:length(unique(sample_data$perturbation))])

sample_data$time <- as.numeric(sample_data$time)

usethis::use_data(sample_data, overwrite = TRUE)