chippeakanno package: "getAllPeakSequence" problem

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chippeakanno package: "getAllPeakSequence" problem

Nico902
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.

Thanks.
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Re: chippeakanno package: "getAllPeakSequence" problem

Uwe Ligges-3


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.

Best,
Uwe Ligges








>
>
> Is the error coming from my configuration or from the code? I do not know
> many things about OOP in R.
>
> Thanks.
>
> --
> View this message in context: http://r.789695.n4.nabble.com/chippeakanno-package-getAllPeakSequence-problem-tp3830284p3830284.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
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Re: chippeakanno package: "getAllPeakSequence" problem

Martin Morgan
In reply to this post by Nico902
On 09/21/2011 08:08 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.

Hi Nico902

Please ask questions about this Bioconductor package on the Bioconductor
mailing list.

http://bioconductor.org/help/mailing-list/

Likely your packages are not at a consistent version. Follow these
instructions

http://bioconductor.org/install/#update-bioconductor-packages

to update your packages.

Martin

>
> Thanks.
>
> --
> View this message in context: http://r.789695.n4.nabble.com/chippeakanno-package-getAllPeakSequence-problem-tp3830284p3830284.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: chippeakanno package: "getAllPeakSequence" problem

David Winsemius
In reply to this post by Nico902

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

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: chippeakanno package: "getAllPeakSequence" problem

Nico902
In reply to this post by Martin Morgan
Thanks Martin, it worked.

I will post on BioC next time.

Cheers.