I'm using r3Cseq Version: 1.16.0 (Built with R 3.2.2).
I'm trying to use this in batch mode and I found the following problem:
1. I do not have controls, I have 2 experimental files. When I initialize my batch object, even though I set the argument isControlInvolved to FALSE, I still get an error if I do not provide the arguments contrBatchLabel and BamContrFiles, e.g.
Error in validObject(.Object) :
invalid class “r3CseqInBatch” object: Please enter the list of BAM file names in the controls
2. I then tried to provide these arguments with NA values: contrBatchLabel=NA,BamContrFiles=NA in the constructor. If I do this I no longer get an error, but when I then try to run
Error in file.exists(i.file) : invalid 'file' argument
it complains. I have checked that the experimental files provided and their path were not misspelled, so I imagine that the problem is relating to the missing control files.
Can you suggest how to get around this problem?