Warning and Error Handling with tryCatch()

A few weeks ago, I worked on an implementation of Fisher’s exact test in R. The script expects a data frame with rows representing the various cases/phenotype of my bacterium, and columns corresponding to the presence or absence of certain genes as detected by SRST2. Fisher’s exact test, which is said to work well with small sample sizes, examines the association between two categorical variables (e.g. whether the presence or absence of a gene is linked to the manifestation of a phenotype). Implementing it in R was a matter of calling the fisher.test() function on a 2x2 contingency table called count.df to generate the p-values:

pval <- fisher.test(count.df,alternative="two.sided")$p.value

But alas, it wasn’t that easy since some of my count tables certainly had only one row or column (i.e. lack of intersection between the variables); hence, this error message in the console:

Error in fisher.test(count.df, alternative = "two.sided") : 'x' must have at least 2 rows and columns

I had to look for a way to ignore the errors and print NA instead. This is where the tryCatch() function comes in: it provides a mechanism for handling unusual conditions, including errors and warnings. tryCatch() follows the following syntax:

output <- tryCatch({expr}, warning = function(w) {warning-handler-code}, error = function(e) {error-handler-code})

1. {expr}: Expression to be evaluated
2. warning = function(w) {warning-handler-code}: Handles the warnings, wherein {warning-handling-code} is the alternative value to be returned when {expr} generates a warning
3. error = function(e) {error-handler-code}: Handles the errors, wherein {error-handler-code} is the alternative value to be returned when {expr} generates an error

For my implementation of Fisher’s exact test to work, I wrapped my original expression with the tryCatch() function, so that every time an error is encountered, it returns NA:

pval <- tryCatch(fisher.test(count.df,alternative="two.sided")$p.value, error=function(e) NA)