Chunk #50 — Materials and Methods — Statistical inference — False discovery rate

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GPA: a statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation.

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After we estimate the parameters in the GPA model, SNPs can be prioritized based on their local false discovery rates [50]. Note that separate analysis of single GWAS data based on their summary statistics is equivalent to the analysis of single GWAS data using GPA without any annotation data. Hence, separate analysis of single GWAS data can be considered as a special case of our GPA approach.