Scripts for manuscript "Cross tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder"
Available here: https://www.nature.com/articles/s41467-017-00868-y
Directory descriptions:
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meQTLParameters: Implement data-driven procedure to select meQTL query parameters (window size, MAF threshold, DNAM sd threshold) to ensure adequate power for SNP & DNAm data
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meQTLScreening&FDR: Perform meQTL query and implement procedure to control meQTL FDR
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SNPBasedEnrichment: Perform analysis to examine if ASD-related SNPs are enriched for meQTLs, across tissue type
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GOBasedEnrichment: Examine which biological pathways are over-represented by meQTL targets of ASD SNPs and meQTL targets generally, across tissue type
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GWASLociExpansion: Demonstrate utility of meQTL target information to enhance regions implicated by GWAS SNP positions
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RegulatoryFeatureEnrichment: Determine which DNaseI HS sites, chromatin marks, and TFBSs that meQTL targets of pyschiatric disorder-related SNPs, and meQTL targets generally, preferentially overlap