Hi, I am trying to create a GRanges list object for all the features of a transcript database created from the GENCODE gtf file. I have created GRanges object for the features "exons","genes","transcripts","introns". When I try to combine these individual objects into a GRangesList, I get the following error: >grl<-GRangesList("genes"=genes.gencode,"transcripts"=transcript.genco de) Error in .Method(..., deparse.level = deparse.level) : number of columns for arg 2 do not match those of first arg Detailed steps I have used in creating the transcriptDb object and extraction of features is identical to the procedure followed in this blog post <http: chitka-kalyan.blogspot.com="" 2014="" 02="" creating-gencode-="" transcript-database-in.html=""> I would appreciate if somebody could help me solve this! Regards, Kalyan [[alternative HTML version deleted]]

GRangesList asserts that all GRanges have the same set of metadata columns (mcols). GenomicRangesList, which does not have that constraint, is the appropriate container in this case. Michael On Wed, Feb 26, 2014 at 12:50 AM, Kalyan K Pasumarthy <kalyankpy@gmail.com>wrote: > Hi, > > I am trying to create a GRanges list object for all the features of a > transcript database created from the GENCODE gtf file. I have created > GRanges object for the features "exons","genes","transcripts","introns". > When I try to combine these individual objects into a GRangesList, I get > the following error: > > >grl<-GRangesList("genes"=genes.gencode,"transcripts"=transcript.gen code) > Error in .Method(..., deparse.level = deparse.level) : > number of columns for arg 2 do not match those of first arg > > Detailed steps I have used in creating the transcriptDb object and > extraction of features is identical to the procedure followed in this blog > post > < > http://chitka-kalyan.blogspot.com/2014/02/creating-gencode- transcript-database-in.html > > > > I would appreciate if somebody could help me solve this! > > Regards, > Kalyan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]