102 patternmarkers all returning empty lists

FertigLab / CoGAPS

Bayesian MCMC matrix factorization algorithm

https://www.bioconductor.org/packages/release/bioc/html/CoGAPS.html

BSD 3-Clause "New" or "Revised" License

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102 patternmarkers all returning empty lists #103

Closed dimalvovs closed 3 months ago

dimalvovs commented 4 months ago

add a test that fails on empty patterMarkers
make it pass by rewriting the method for threshold='all'

dimalvovs commented 4 months ago

@kwoyshner can you review please?

kwoyshner commented 4 months ago

I tried reinstalling from this branch and was able to get patternMarkers with 'all' now, thank you!

dimalvovs commented 4 months ago

@kwoyshner do you want to have a look at threshold = 'cut'? I've updated it too. This part of code is poorly documented so I was not sure what that mode should do but there was a dimension mismatch. simplicityGENES function needs to be inspected for functionality.