Question

Can someone help me with this piece of code. In a loop I’m saving p-values in f and then I want to write the p-values to a file but I don’t know which function to use to write to file. I’m getting error with write function.

{
f = fisher.test(x, y = NULL, hybrid = FALSE, alternative = "greater",
                conf.int = TRUE, conf.level = 0.95, simulate.p.value = FALSE)

write(f, file="fisher_pvalues.txt", sep=" ", append=TRUE)
}

Error in cat(list(...), file, sep, fill, labels, append) : 
  argument 1 (type 'list') cannot be handled by 'cat'

Answer 1

The return value from fisher.test is (if you read the docs):

Value:

 A list with class ‘"htest"’ containing the following components:

p.value: the p-value of the test.

conf.int: a confidence interval for the odds ratio. Only present in
the 2 by 2 case and if argument ‘conf.int = TRUE’.

etc etc. R doesn’t know how to write things like that to a file. More precisely, it doesn’t know how YOU want it written to a file.

If you just want to write the p value, then get the p value and write that:

 write(f$p.value,file="foo.values",append=TRUE)