Thanks a lot! That solved the problem :-) 2013/1/23 Michael Lawrence <lawrence.michael@gene.com> > 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 >> > > -- *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 [[alternative HTML version deleted]]