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HenrikBengtsson / PSCBS

🔬 R package: Analysis of Parent-Specific DNA Copy Numbers
https://cran.r-project.org/package=PSCBS
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SPEEDUP: Profile to find bottlenecks #38

Closed HenrikBengtsson closed 6 years ago

HenrikBengtsson commented 6 years ago

There are lots of internal, repetitive validation done over and over. Also lots of repeated lookups and package loading/attaching. Should be room for memoization.

Run time profiling.

HenrikBengtsson commented 6 years ago

profvis::profvis() says that we spent most (> 95%) of the time in DNAcopy::segment()* so not much we can do in PSCBS. (*) ... which in turn spends the majority of its time in native Fortran code.