[R] chippeakanno package: "getAllPeakSequence" problem
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.
> Is the error coming from my configuration or from the code? I do not know
> many things about OOP in R.
> View this message in context: http://r.789695.n4.nabble.com/chippeakanno-package-getAllPeakSequence-problem-tp3830284p3830284.html
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> and provide commented, minimal, self-contained, reproducible code.
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