Implement FDR calculation#2
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krassowski wants to merge 4 commits into
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as suggested by @ivokwee in gravitino#1
to achieve results closer to those of the original GSEA
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Hi @gravitino,
First off, thank you for maintaining this package!
During my MRes project I implemented FDR calculation for cudaGSEA. I was wondering if you are interested in merging my changes in. I have tested the results against the GSEADesktop (from Broad Institute) and it looks quite good (the grey line is the GSEADesktop FDR;
cuda_full_fdr- the second facet - is the implementation that I propose in this PR):I also implemented an "approximate" FDR procedure (one-sided, please see with_approximate_fdr branch, here is the diff) which is slightly faster but is not a part of this PR. The other branch also comes with a command line option for switching the FDR calculation - I can include it in this PR if you wish.
Please let me know what you think - I may be able to find some time to polish the code if you consider it worth merging.