R Error When Running Exomedepth

Question

[datanerd]

Hi all, I have a problem when running Exomedepth when creating my Reference set

" myreferenceset <- as.matrix(mycount[,myrefsamples]) Error in as.vector(data) : no method for coercing this S4 class to a vector"

Could someone help help with what the error might be. Thanks!

[Ying W]

It would be helpful if you posted output of sessionInfo()

Answer 1

[Jeremy Leipzig]

is mycount an ExomeDepth object? what does this return?

str(mycount)

you might want the mycount@CNVcalls slot

[datanerd]

Thank you for the replies. :) It was the problem of mycount. The second time I run the program it somehow gave me empty mycount (although when I was checking to see if the program is running fine, it did return mycount objeect). The program is running fine(m happy). Thanks again.