R/OERmodel.R

In bhklab/RadioGx: Analysis of Large-Scale Radio-Genomic Data

# OER function for a given hypoxic concentration by the user
#
# @param oxygenConc \code{numeric} An oxygen concentratio between 0.1 and 10
#
# @return \code{none} Generates a dose response curve for a given hypoxic
#   concentration
#
OERmodel <- function(oxygenConc) {

  pO2 <- oxygenConc
  pO2 <- as.numeric(pO2)
  if (is.na(pO2)) {
    stop("Error: oxygenConc is NA!")}

  if (pO2<0.1 | pO2>10){
    stop("Please enter an oxygenConc between 0.1 and 10!")
  }

  OER_m = 3
  K_m = 3
  a = ((OER_m*pO2)+K_m)/(pO2+K_m)
  OMF = (1/OER_m)*a

  D <- seq(0, 10, 1)
  SF1 = exp(-0.3*D*OMF-(0.03*D*D*OMF))
  pdf("HyxpoxiaPlot.pdf")
  RadioGx::doseResponseCurve(Ds=list("Hypoxia" = D),
                              SFs=list("Hypoxia" = SF1), plot.type="Actual",
                              legends.label = NULL,title = "Effect of Hypoxia",
                              cex = 1.55,cex.main = 1.75,lwd = 2)
  dev.off()
}