"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]]