I am having trouble with memory usage and the SWATH2stats R package. Specifically, when I attempt to split the transition groups into single transitions (in order to go on to use MSstats or MapDIA), using:
data.transition <- disaggregate(data.filtered)
error: cannot allocate vector of size 7.0Gb
The data has been processed through the OpenSwathWorkflow, and reports ~4,000 protein ID hits, with ~16,000 unique peptides, and ~70,000 transitions . I have filtered and reduced the data using SWATH2stats, however it is for global profiling, so I do expect relatively high numbers.
Aside from increasing RAM (I am currently running 64-bit R, on Windows 7, with 32GB RAM), I was wondering if there are any work-arounds with SWATH2stats when dealing with data as large as this? Or whether any alternative tools are be better suited?
Any advice or tips appreciated!