R/chisq.test2.R

In ZhonghuiGai/groutable: This is a wrapper function of compareGroups package

chisq.test2 <-
  function(obj, chisq.test.perm, chisq.test.B, chisq.test.seed){

    if (any(dim(obj)<2) || is.null(dim(obj)) || sum(rowSums(obj)>0)<2 || sum(colSums(obj)>0)<2)
      return(NaN)
    obj<-obj[,colSums(obj)>0] # erase columns full of zeros.
    expect<-outer(rowSums(obj),colSums(obj))/sum(obj)
    if (any(expect<5)){
      if (chisq.test.perm){
        if (!is.null(chisq.test.seed)) set.seed(chisq.test.seed)
        test<-try(chisq.test(obj, simulate.p.value=chisq.test.perm, B = chisq.test.B),silent=TRUE)
      } else
        test <- try(fisher.test(obj),silent=TRUE)
    } else {
      test <- try(chisq.test(obj),silent=TRUE)
    }
    if (inherits(test,"try-error"))
      return(NaN)
    ans <- test$p.value

    ans
  }