Chisq-test in R and tryCatch() function

Question

[Jonathan Yoou]

Hi all,

I'm currently working with gene presence/absence data from 2 different groups. So I'm making a code to test their independence with chisq.test in R, but I don't know why tryCatch() function in R doesn't work I expected. Below is the code:

tryCatch(
    chi_result <- pairwiseNominalIndependence(table(temp_df), chisq=TRUE, method="bonferroni"),
    pval <- chi_result[["p.Chisq"]],
    pval_adj <- chi_result[["p.adj.Chisq"]],
    error=function(e){
      chi_result <- chisq.test(table(temp_df))
      pval <- chi_result[["p.value"]]
      pval_adj <- "INVALID INPUT"
      }
  )

What I intend is, pairwiseNominalIndependence() function makes an error, "Error in [.default(x, j, ) : subscript out of bounds", if every genes exist or absent, so I want to run chisq.test instead if pairwiseNominalIndependence() provokes an error cuz it results in nonsignificant p-value as an output anyway. If I run every each line by line, every code works perfectly, but if I run the tryCatch chunk, it doesn't run chisq.test(table(temp_df) and results in pval as NULL. Can someone give me any comment on it?

Thank you in advance

Answer 1

[Ram]

You're using tryCatch() wrong - the code to try should be in a block, and the code to execute on error should be in a separate block. You're doing the latter but not the former. See:

tryCatch(
    {
    chi_result <- pairwiseNominalIndependence(table(temp_df), chisq=TRUE, method="bonferroni");
    pval <- chi_result[["p.Chisq"]];
    pval_adj <- chi_result[["p.adj.Chisq"]];
    }, 
    error=function(e){
      chi_result <- chisq.test(table(temp_df))
      pval <- chi_result[["p.value"]]
      pval_adj <- "INVALID INPUT"
      }
  )

See here for a more comprehensive example.

As a side note, you could have Googled before posting and made sure you were using the right syntax.