Question: r3Cseq problems in batch mode
0
gravatar for manduchi
3.4 years ago by
manduchi0
manduchi0 wrote:

Hello,

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

getBatchRawReads(my3Cbatch)
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?

Thanks

 

 

 

 

contrBatchLabel=NA,BamContrFiles=NA

r3cseq • 521 views
ADD COMMENTlink modified 2.2 years ago by izzy.yichao.cai10 • written 3.4 years ago by manduchi0
Answer: r3Cseq problems in batch mode
0
gravatar for izzy.yichao.cai
2.2 years ago by
izzy.yichao.cai10 wrote:

I have the same problem. Did you figure it out?

ADD COMMENTlink written 2.2 years ago by izzy.yichao.cai10
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