search

UW-GAC / GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
https://bioconductor.org/packages/GENESIS
34 stars 13 forks source link

Available rare variant aggregate association tests #113

Closed CristianRiccio closed 3 months ago

CristianRiccio commented 3 months ago

Hello, Are these the available rare variant aggregate association tests? BinomiRare, burden, CMP test, fastSKAT, fastSMMAT, SKAT, SKAT-O, SMMAT

and are BinomiRare, CMP test, Score, SPA test the tests available for single-marker tests?

Does BinomiRare aggregate variants in a set or testing unit? How can I choose the testing unit?

Thanks, and best wishes, Cristian.

smgogarten commented 3 months ago

That is correct. All the aggregate tests define testing units with a SeqVarIterator object, which can be defined in various ways: blocks, sliding windows, and GRanges objects. See the documentation in the SeqVarTools package for more information on how to construct these objects.