Dear all, I am getting error when i try to read .bam files. The problem is that i don't understand what does not it mean and what I do to solve it. here's the error. " Error in queryHits(findOverlaps(query, subject, maxgap = maxgap, minoverlap = minoverlap, : error in evaluating the argument 'x' in selecting a method for function 'queryHits': Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘findOverlaps’ for signature ‘"list", "GappedAlignments"’ " I would appreciate any help. Regards -- Reema Singh PhD Scholar Computational Biology and Bioinformatics School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi-110067 INDIA [[alternative HTML version deleted]]

On 06/01/2013 07:46 AM, Reema Singh wrote: > Dear all, > > I am getting error when i try to read .bam files. The problem is that i > don't understand what does not it mean and what I do to solve it. here's > the error. > > " > Error in queryHits(findOverlaps(query, subject, maxgap = maxgap, minoverlap > = minoverlap, : > error in evaluating the argument 'x' in selecting a method for function > 'queryHits': Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?findOverlaps? for > signature ?"list", "GappedAlignments"? this is saying that findOverlaps does not know what to do when you provide a 'list' as it's first argument, and a 'GappedAlignments' as its second argument. Probably the problem is how you created the 'query' object; aim for one of the data types indicated by showMethods(findOverlaps) Martin > " > > I would appreciate any help. > > Regards > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

Hi Reema, On 06/01/2013 07:46 AM, Reema Singh wrote: > Dear all, > > I am getting error when i try to read .bam files. The problem is that i > don't understand what does not it mean and what I do to solve it. here's > the error. > > " > Error in queryHits(findOverlaps(query, subject, maxgap = maxgap, minoverlap > = minoverlap, : > error in evaluating the argument 'x' in selecting a method for function > 'queryHits': Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?findOverlaps? for > signature ?"list", "GappedAlignments"? > " In addition to showing us the error, could you also show us the code that produces it please? I'm surprised you get this error when trying to read .bam files since AFAIK reading .bam files with the standard tools (i.e. readGappedAlignments or readGappedAlignmentPairs) doesn't involve calls to findOverlaps(). Thanks, H. > > I would appreciate any help. > > Regards > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319