2021
DOI: 10.1101/2021.05.16.21257289
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Cross-GWAS coherence test at the gene and pathway level

Abstract: We devise a significance test for covariance of samples not drawn independently, but with known inter-sample covariance structure. The test distribution we propose is a linear combination of χ2 distributions, with positive and negative coefficients. The corresponding cumulative distribution function can be efficiently calculated with Davies algorithm at high precision. As an application, we propose a test for dependence between SNP-wise effect sizes of two genome-wide association studies at the level of genes.… Show more

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“…All calculations were performed with the python package PascalX [17], which incorporates the methods detailed in the Methods section (see also Code availability statement). The association directions were extracted from the signs of the raw effect sizes (β).…”
Section: Covid-19 Gwas Applicationmentioning
confidence: 99%
“…All calculations were performed with the python package PascalX [17], which incorporates the methods detailed in the Methods section (see also Code availability statement). The association directions were extracted from the signs of the raw effect sizes (β).…”
Section: Covid-19 Gwas Applicationmentioning
confidence: 99%