tryCatch does not seem to return my variable

Question

I'm trying to use tryCatch to generate a list of p-values there are several rows in the matrix that don't have enough observations for a t test. Here is the code I generated so far:

pValues <- c()
for(i in row.names(collapsed.gs.raw)){
  tryCatch({
    t <- t.test(as.numeric(collapsed.gs.raw[i,]) ~ group)
    pValues <- c(pValues, t$p.value)
  },
  error = function(err) {
    pValues <- c(pValues, "NA")
    message("Error")
    return(pValues)
  })}

It definitely throws an error [I put in the message("Error") line to confirm]. The problem is that the vector pValues doesn't have any "NA" in it, though it should.

Thanks in advance for your help!

Answer 1

The pvalues in your function is a local variable. You might be able to fix this with <<-, but it would be preferred to have the function just return the one desired value and collect them outside the function with sapply. Perhaps something like (untested):

pValues <- sapply(rownames(collapsed.gs.raw), function(i) {
  tryCatch({
    t.test(as.numeric(collapsed.gs.raw[i,]) ~ group)$p.value
  },
  error = function(err) {
    message("Error")
    return(NA)
  })
})