Error Handling in R when implementing association test - r

Question

I am implementing a zero-inflated negative binomial in R. The code is here:
> ICHP<-read.table("ichip_data_recodeA.raw",header=TRUE)
ICHPdt<-data.table(ICHP)
covfile<-read.table("sorted.covfile.to.glm.out",header=TRUE)
covfiledt<-data.table(covfile)
library(pscl)
fhandle<-file("ichip_zi_nb_model_scoretest.csv","a")
for (i in seq(7, ncol(ICHPdt), 1)) {
notna<-which(!is.na(ICHPdt[[i]]))
string<-eval(parse(text = paste("ICHPdt$", colnames(ICHPdt)[i], sep="")))
nullglmmod<-zeroinfl(formula=OverllTot0[notna] ~ EurAdmix[notna] + Sex[notna] + DisDurMonths[notna] + BMI[notna] + Group[notna] + SmokingStatus[notna], data=covfiledt, dist="negbin")
nullsum<-coef(summary(nullglmmod))
glmmod<-zeroinfl(formula=OverllTot0[notna] ~ EurAdmix[notna] + Sex[notna] + DisDurMonths[notna] + BMI[notna] + Group[notna] + SmokingStatus[notna] + ICHPdt[[i]][notna], data=covfiledt, dist="negbin")
summ <- coef(summary(glmmod))
rownames(summ$zero)[8] <- paste0("ICHPdt$", colnames(ICHPdt)[i])
rownames(summ$count)[8] <- paste0("ICHPdt$", colnames(ICHPdt)[i])
writeLines("zero", con=fhandle)
writeLines(colnames(ICHPdt)[i], fhandle)
write.table(round(summ$zero, 4), file=fhandle)
writeLines("count", con=fhandle)
writeLines(colnames(ICHPdt)[i], fhandle)
write.table(round(summ$count, 4), file=fhandle)
}
The script errors when i=9246, and issues the following:
Error in solve.default(as.matrix(fit$hessian)) :
system is computationally singular: reciprocal condition number = 1.12288e-19
Overall, I need to go through ~100,000 markers, so I should expect ~11 such errors.
I would like to help implementing options, for instance with tryCatch() for catching such an error, skipping that marker, and moving on.

Answer 1

I recommend reading this page for a quick primer and this page for a more complete explanation of error handling, and you should eventually read ?conditions, but in short, there are two ways to handle errors. The first is with a try-catch, as in:
AS.NUMERIC <- function(x){
# for use in the warning handler
expectedWarning <- FALSE
result = tryCatch({
# a calculation that might raise an error or warning
as.numeric(x)
}, warning = function(w) {
# the typical way to identify the type of
# warning is via it's message attribure
if(grepl('^NAs introduced by coercion',w$message)){
cat('an expected warning was issued\n')
# assign the expected value using the scoping assignment
expectedWarning <<- TRUE
}else
cat('an unexpected warning was issued\n')
# reissue the warning
warning(w)
}, error = function(e) {
cat('an error occured\n')
# similar things go here but for handling errors
}, finally = {
# stuff goes here that should happen no matter what,
# such as closing connections or resetting global
# options such as par(ask), etc.
})
# you can handle errors similarly
if(expectedWarning)
result <- 5
return(result)
}
AS.NUMERIC('5')
#> [1] 5
AS.NUMERIC('five') # raises a warning
#> an expected warning was issued
#> [1] 5
#> Warning message:
#> In doTryCatch(return(expr), name, parentenv, handler) :
#> NAs introduced by coercion
The second way is to use try(), which is less nuanced:
x = try(stop('arbitrary error'),# raise an error
silent=TRUE)
# if there is an error, x will be an object with class 'try-error'
if(inherits(x,'try-error'))
# set the default value for x here
x = 5