Hello! Does anyone know how to save GRangesList object to a file? And how to convert it to a GFF file? Thank you! Best, Milica [[alternative HTML version deleted]]

On Mon, Mar 26, 2012 at 6:47 AM, Milica Krunic <milica.crown@gmail.com>wrote: > Hello! > > > Does anyone know how to save GRangesList object to a file? And how to > convert it to a GFF file? > > You can save any R object to a file using save(), so please read the documentation on that (?save) ... it saves the contents of the object in an R-oriented format, for later restoration using load(). To save content of a GRangesList to a GFF file, use the export() methods of rtracklayer. I don't think you can export a GRangesList directly, but apply unlist() first, and use code like that given with ?export, in the examples section, in which a connection and export format is defined. Thank you! > > > Best, > Milica > > [[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]]

On Mon, Mar 26, 2012 at 3:47 AM, Milica Krunic <milica.crown@gmail.com>wrote: > Hello! > > > Does anyone know how to save GRangesList object to a file? And how to > convert it to a GFF file? > > As Vince mentioned, it is possible to use rtracklayer::export() to generate a GFF file. In devel (soon to be released), you can simply pass the GRangesList to export. Behind the scenes, this calls asGFF() to get a GRanges with the metadata columns that encode the hierarchical structure according to the GFF3 spec. This is then converted to a RangedData and exported. Michael > Thank you! > > > Best, > Milica > > [[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]]