inst/unitTests/test_simData.R

In simulatorZ: Simulator for Collections of Independent Genomic Data Sets

test_simData <- function(){
  library(curatedOvarianData)
  data(E.MTAB.386_eset) 
  origin_esets <- list(E.MTAB.386_eset)
  balance.variables="tumorstage"
  simmodel <- simData(obj=origin_esets, 
                      balance.variables=balance.variables,
                      n.samples=150, type="one-step")  
  new_esets <- simmodel$obj
  covariates.origin <- lapply(origin_esets, function(eset){
    if(length(balance.variables) == 1){
      return(as.character(pData(eset)[, balance.variables]))
    }
    else{
      return(as.character(do.call(paste, pData(eset)[, balance.variables])))
    }
  })
  covariates.originall <- do.call(c, covariates.origin)
  covariates.sim <- lapply(new_esets, function(eset){
    if(length(balance.variables) == 1){
      return(as.character(pData(eset)[, balance.variables]))
    }
    else{
      return(as.character(do.call(paste, pData(eset)[, balance.variables])))
    }
  }) 
  freq.sim <- freq.origin <- c()
  for(i in seq_along(covariates.sim)){
    id <- match(covariates.sim[[i]], covariates.originall)
    freq.sim <- table(covariates.sim[[i]]) / sum(table(covariates.sim[[i]]))
    freq.origin <- table(covariates.originall[id]) / sum(table(covariates.originall[id]))    
  }
  checkEqualsNumeric(as.numeric(freq.sim), as.numeric(freq.origin))
  #checkEqualsNumeric(simmodel$prob.desired, simmodel$prob.real[[1]])
}