Hello,

I am looking for a method in R to check a list of accession numbers against annotation databases for 19 species. In theory the code below should extract the ENTREZID, SYMBOL, GENENAME and match the mapped results with the results file via the ACCNUM

mapped <- foreach(i = dbMap$dbName) %do% select(i, as.character(ResultsFile$ACCNUM), c("ENTREZID","SYMBOL","GENENAME"), "ACCNUM")

However select is throwing the error:

Error in select(i, as.character(ResultsFile$ACCNUM), c("ENTREZID", "SYMBOL",  : 
  task 1 failed - "unable to find an inherited method for function ‘select’ for signature ‘"factor"’

This is because i is a factor with 19 levels (one for each database). How could I coerce this to work and produce the desired results?

Thanks for your time and help,

Morgan

Ideally you wouldn't start with a factor, so when you create your data.frame (however you are doing that), you would want to use stringsAsFactors = FALSE. Also note that select expects you to pass an OrgDb, not a character value that has the same name as an OrgDb, so you need to get the OrgDb. Something like this

mapped <- foreach(i = get(dbMap$dbName)) %do% select(i, as.character(ResultsFile$ACCNUM), c("ENTREZID","SYMBOL","GENENAME"), "ACCNUM")

And having ResultsFile$ACCNUM already being a character is one less coercion you need to worry about.