Transcription of GEMMA User Manual
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GEMMA User Manual
GEMMA User Manual Xiang Zhou May 18, 2016. Contents 1 Introduction 4. What is GEMMA .. 4. How to Cite GEMMA .. 4. Models .. 5. Univariate Linear Mixed Model .. 5. Multivariate Linear Mixed Model .. 5. Bayesian Sparse Linear Mixed Model .. 6. Variance Component Models .. 7. Missing Data .. 7. Missing Genotypes .. 7. Missing Phenotypes .. 8. 2 Installing and Compiling GEMMA 9. 3 Input File Formats 10. PLINK Binary PED File Format .. 10. BIMBAM File Format .. 11. Mean Genotype File .. 11. Phenotype File .. 12. SNP Annotation File (optional) .. 12. Relatedness Matrix File Format .. 13. Original Matrix Format .. 13. Eigen Value and Eigen Vector Format .. 14. Covariates File Format (optional) .. 14. Beta/Z File .. 15. Category File .. 15. LD Score File .. 15. 1. 4 Running GEMMA 17. A Small GWAS Example Dataset .. 17. SNP filters .. 17. Association Tests with a Linear Model.
May 18, 2016 Contents ... Nature Genetics. 44: 821-824. Multivariate linear mixed models Xiang Zhou and Matthew Stephens (2014). E cient multivariate linear mixed model algo- ... where y is an n-vector of quantitative traits (or binary disease labels) for nindividuals; W = (w
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