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remove dependency of ‘TCGAbiolinks’.
getMutex and getMutexAB computes the exact p-value using the ShiftConvolvePoibin R package (Peres, N., Lee, A., and Keich, U.,2020). Mixed and exact have been enhanced in terms of speed and memory usage.
getMutex and getMutexAB have three different approximations of the Poison-Binomial distribution function: a “RefinedNormal”” Approximation (Volkova, 1996), “Binomial”” with two parameters (Cam, 1960), and a “Shifted Binomial” with three parameters (Peköz, Shwartz, Christiansen, & Berlowitz, 2010). This last is the approximation by default for both functions. Moreover, some bugs have been fixed.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.