benchmarking out-of-memory strategies for R
Purpose is to allow comparison of timings of operations on NRxNC matrix: wr is write to store, ingFull is ingest from store, ing1K is ingest 1000 rows.
> benchOOM(times=2)
NR NC times meth wr ingFull ing1K units
1 5000 100 2 hdf5 17.07860 5.084726 6.266323 microsec
2 5000 100 2 ff 189.67263 66.584151 2.393100 microsec
3 5000 100 2 sqlite 125.93066 134.882089 24.409271 microsec
4 5000 100 2 data.table 25.58902 8.639789 4.963109 microsec
5 5000 100 2 bigmemory 29.09477 1.592431 0.756485 microsec
Also includes tentative work on exporting assay data from a RangedSummarizedExperiment as a DelayedArray with HDF5 back end.