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privefl / bigsnpr

R package for the analysis of massive SNP arrays.
https://privefl.github.io/bigsnpr/
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Inflated Q-Q #421

Closed boseb closed 1 year ago

boseb commented 1 year ago

Hi Florian, I am using the function pkg.paper.PRS::get_pheno to generate binary phenotypes. If I select causal variants to be spread across the multiple chromosomes (5 chromosomes) with default parameters, the q-q plot from logistic regression (from PLINK) gets highly inflated. Do you have any recommendations about how to use the parameters of this function to control this issue?

Thanks, Bose

privefl commented 1 year ago

Have a look at https://www.nature.com/articles/ejhg201139

Here, we show by theory, simulation and analysis of data that in the absence of population structure and other technical artefacts, but in the presence of polygenic inheritance, substantial genomic inflation is expected.

privefl commented 1 year ago

Any update on this?