[R] chippeakanno package: "getAllPeakSequence" problem

David Winsemius dwinsemius at comcast.net
Wed Sep 21 17:23:14 CEST 2011

On Sep 21, 2011, at 11:08 AM, Nico902 wrote:

> Hi all,
> I am using the package ChIPpeakAnno, and I have a problem with the  
> function
> getAllPeakSequence. This is related to object oriented programming I  
> think,
> I have the following message:
>> peaksWithSequences <- getAllPeakSequence(peakList, upstream = 100,
>> downstream = 100, genome = Hsapiens)
> Error in validObject(.Object) :
>  invalid class "GRanges" object: superclass "Sequence" not defined  
> in the
> environment of the object's class
> Is the error coming from my configuration or from the code? I do not  
> know
> many things about OOP in R.

I haven't ever seen that package mentioned on r-help befor, so it is  
probably a BioC package. Bioconductor which has its own mailing list.  
There are a small number of persons who are bicultural with ordinary-R  
and BioC, but they generally suggest to posters to use the BioC list.  
(I don't know if it has a Nabble interface. I'm guessing it does not.)


David Winsemius, MD
West Hartford, CT

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