Re: [Bioc-devel] Reducing memory footprint of large object

gdsfmt is another option for storing large datasets on disk, similar to HDF5. Take a look at packages SNPRelate, GWASTools and SeqArray which all use it to store genotype data. Stephanie On 11/5/15 8:41 AM, Fischer, Bernd wrote: Hi Christian, you should have a look at packages that for parti

[Bioc-devel] Moving from MakeOrganismPackage to AnnotationHub recipes

Hello, I have started putting together an AnnotationHub recipe for the TriTrypDB . The goal is to write a generalized recipe which can then be adopted for all of the other EuPathDB databases. I curently have code for generating OrgD

Re: [Bioc-devel] Base class for interaction data - expressions of interest

There's a growing number of Bioconductor packages dealing with interaction data; diffHic, GenomicInteractions, HiTC, to name a few (and probably more in the future). Each of these packages defines its own class to store interaction data - DIList for diffHic, GenomicInteractions for GenomicInter

Re: [Bioc-devel] Reducing memory footprint of large object

Hi Christian, you should have a look at packages that for partial reading of data, like e.g. big memory that only load data partially in memory or implement partial reading yourself using HDF5 and rhdf5. Best, Bernd > On 05.11.2015, at 16:22, Christian Arnold wrote: > > > Hi all, > > I wa

[Bioc-devel] Reducing memory footprint of large object

Hi all, I wanted to ask around in this list with full of experts if any of you have an advice about the following problem: I got a large SNPhood object from someone (package SNPhood, which I developed) from an analysis of 200.000 SNPs or so that stores lots of read counts and the positions