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xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
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variant set in gene-centric coding/noncoding analysis #65

Closed eliu98 closed 1 month ago

eliu98 commented 1 month ago

Hi Dr. Li,

I am running the STAARPipeline with a relatively small sample size (~1000 samples), which limits the number of rare variants in the rare variant set, especially when they are grouped based on their functional annotations. Is there a way to combine/customize the variants sets before testing (i.e. I'd like to combine the pLof and missense variants for each gene so that I will have more variants in each variant set)?

Also, how is the alpha levels determined in the sliding window and dynamic window analyses?

Thank you!

Best, Elaine

xihaoli commented 1 month ago

Dear Elaine,

Thanks for your questions. Yes, while developing and maintaining STAARpipeline, we have expanded its usage by allowing for (1) combining and (2) customizing the variant sets before testing. Currently, these additional functionalities are in the final testing and polishing stage. Please send a note for me to share so that you can make use of it.

Your question on the alpha levels determined in the sliding window and dynamic window analyses is answered in #31.

Best, Xihao

eliu98 commented 1 month ago

Thank you!