Chunk #61 — Methods — MAGMA primary and conditional analyses

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Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson's disease.

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To test whether MAGMA was well-calibrated, we randomly permuted the gene labels of the schizophrenia gene-level association statistic file a thousand times. We then looked for association between the 10% most specific genes in each cell type and the randomized gene-level schizophrenia association statistics. We observed that MAGMA was slightly conservative with less than 5% of the random samplings having a P-value <0.05 (Figure S26).