[R] chippeakanno package: "getAllPeakSequence" problem

Uwe Ligges ligges at statistik.tu-dortmund.de
Wed Sep 21 17:19:51 CEST 2011

On 21.09.2011 17:08, 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

We do not know, since we do not know what your objects "peakList" and 
"Hsapiens" are, hence we cannot reproduce anything here. The example 
works fine for me.

Moreover, please ask question related to BioConductor packages on the 
BioC mailing list.

Uwe Ligges

> Is the error coming from my configuration or from the code? I do not know
> many things about OOP in R.
> Thanks.
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