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Chunk #67 — Methods — Rank-rank hypergeometric overlap (RRHO)

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A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles.
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We assessed genetic relationship between two disorders (rg) by using genetic correlation analysis of LDSC45. To provide similar metrics based on gene-level association statistics, we compared ranks between two datasets (e.g. H-MAGMA outcomes from two disorders) using an R package RRHO (https://www.bioconductor.org/packages/release/bioc/html/RRHO.html) with the following command line: RRHO(<Ranked gene list 1>, <Ranked gene list 2>, outputdir=<output directory>, alternative=“enrichment”, BY=TRUE, log10.ind=TRUE)