The UCSC genome browser prefixes all chromosome names with "chr". So you
need to use renameSeqlevels on your GRanges, first.

Michael


On Wed, Jan 23, 2013 at 5:03 AM, Silvia von der Heyde <
silvia.heyde@gmail.com> wrote:

> "annotated_peaks" is may RangedData object with peak information. If I say
> session<-browserSession()
> genome(session)<-"mm10"
> gr<-as(annotated_peaks, "GRanges")
> view <- browserView(session, gr)
> I get the error
> Error in normGenomeRange(range, object) :
>   'range' has invalid chromosome: 1
> or
> session$peaks<-annotated_peaks
> results in
> Error in FUN(X[[1L]], ...) :
>   Invalid chromosomes for mm10: 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
> 2, 3, 4, 5, 6, 7, 8, 9, X, Y
>
>
> 2013/1/23 Michael Lawrence <lawrence.michael@gene.com>
>
>> Would you please clarify the problem about it being a factor? Some
>> example code and error would help. Also, please keep these types of
>> questions on the bioc list (cc'd).
>>
>> Thanks,
>> Michael
>>
>>
>>
>> On Wed, Jan 23, 2013 at 4:38 AM, Silvia von der Heyde <
>> silvia.heyde@gmail.com> wrote:
>>
>>> Hi!
>>>
>>> I would like to use rtracklayer() to view my peak regions from ChIPseq
>>> analysis in UCSC browser.
>>> It seems to be a problem that the chromosome space is factor in the
>>> RangedData object containing my peak regions. So I wanted to use
>>> as.character() but obviously RangedData enforces the factor level. Do you
>>> know a solution?
>>>
>>> Many thanks in advance,
>>> Silvia
>>>
>>> --
>>> *Silvia von der Heyde*
>>> Universitätsmedizin Göttingen
>>> Abteilung Medizinische Statistik
>>> http://www.ams.med.uni-goettingen.de/amsneu/
>>> E-Mail: Silvia.Heyde@med.uni-goettingen.de
>>> Telefon: 0551-39-10710
>>> Telefax: 0551-39-4995
>>>
>>> Humboldtallee 32
>>> 37073 Göttingen
>>>
>>
>>
>
>
> --
> *Silvia von der Heyde*
> Universitätsmedizin Göttingen
> Abteilung Medizinische Statistik
> http://www.ams.med.uni-goettingen.de/amsneu/
> E-Mail: Silvia.Heyde@med.uni-goettingen.de
> Telefon: 0551-39-10710
> Telefax: 0551-39-4995
>
> Humboldtallee 32
> 37073 Göttingen
>

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