R/gofTest.R

In tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions

gofTest <- function(counts, a=0, mc.cores=1) {
  ff <- function(x) {
    ans <- NA
    suppressWarnings(ans <- try(testShapePT(mlePoissonTweedie(x), a=a), TRUE))
    if (!inherits(ans, "try-error")) {
      ans <- ans$statistic
    } else {
      ans <- NA
    }
    ans
  }
#  haveMulticore <- tweeDEseq:::.isPackageLoaded("multicore")
  if (mc.cores > 1){
                                        #   if(!haveMulticore)
                                        #     stop("In order to run calculations in parallel with multiple cores the 'multicore' library should be loaded first")
                                        #   else{
   # mclapp <- get('mclapply', envir=getNamespace('multicore'))
    countsList <- as.list(as.data.frame(t(counts)))
    gof <- unlist(mclapply(countsList, ff), use.names=FALSE)
                                        #   }
  }
  else
    gof <- apply(counts, 1, ff)
  gof
}