Implemented functions makeDF(), getLimmaInput.DF() and get.pvals.DF() that merge the coverage data into a DataFrame (aka, Rle world from IRanges) saving enough memory space such that it becomes feasible to have all the data in memory and process in chunks from there instead of relying on the sql database.
Currently using the new version with real data from where I'll have a better idea on the time improvements.
Further modified the package so it will pass R CMD check (used check() from the devtools pkg). There are 2 warnings left: 1 is about the license, the other is something related to documentation which I should be able to fix soon.
Missing: implementing a multicore functionality for getLimmaInput.DF
Implemented functions makeDF(), getLimmaInput.DF() and get.pvals.DF() that merge the coverage data into a DataFrame (aka, Rle world from IRanges) saving enough memory space such that it becomes feasible to have all the data in memory and process in chunks from there instead of relying on the sql database.
Currently using the new version with real data from where I'll have a better idea on the time improvements.
Further modified the package so it will pass R CMD check (used check() from the devtools pkg). There are 2 warnings left: 1 is about the license, the other is something related to documentation which I should be able to fix soon.
Missing: implementing a multicore functionality for getLimmaInput.DF