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RajLabMSSM / echofinemap

echoverse module: Statistical and functional fine-mapping functions.
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Check whether fine-mapping method is compatible for quantitative vs. case-control sumstats #18

Open bschilder opened 2 years ago

bschilder commented 2 years ago

Some fine-mapping tools are designed only for case-control studies (e.g GWAS) and can produce biased results if applied with quantitative traits (e.g. height) without further adjustments.

Currently, only ABF() takes the case_control argument. But this should be applied to all other methods where this distinction can be applied. For methods that are unable to handle quantitative traits in an unbiased way, a warning message should be produced letting users know about this. This checking can occur within the check_required_cols() function, which will need an additional argument: case_control

bschilder commented 2 years ago

@AMCalejandro this might be a good second task for you after addressing the verbosity Issue.

AMCalejandro commented 1 year ago

I just had a look into this.

ABF, FINEMAP, PAINTOR, and SuSiE can take SS from cc and qt trait studies.

From SuSiE paper -> https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010299 "Although our derivations and simulations focused on z-scores computed from quantitative traits with a simple linear regression, in practice it is common to apply summary-data fine-mapping methods to z-scores computed in other ways, e.g., using logistic regression on a binary or case-control trait, or using linear mixed models to deal with population stratification and relatedness."

For the rest of the tools, I looked at this Nature Reviews Genetics -> https://www.nature.com/articles/s41576-018-0016-z See table 1

So by reading what you wrote here, we might need to recode the calls to PAINTOR, FINEMAP, SuSiE, and Polyfun and review if they take information regarding the nature of the trait the SSs come from?