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
}
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