Table 2 Summary of the modular pipeline used to analyze data from the UK Biobank
TaskData SetR Package Used
1) Form a linked array with genotypesBGData
2) Determine white British cohortbase
3) SummariesBGData
4) SNP filtering (allele frequency & call rate)base
5) Genomic relationships (GR)BGData
6) Identification of samples with GR < 0.03BGData
7) Computation of 5 PCbase
8) Phenotypes adjustmentsbase
9) Building of training and test setbase
10) GWAS (using adjusted phenotypes)BGData
11) Selection of the top-p variantsbase
12) Bayesian Genomic RegressionBGLR
13) Assessment of prediction accuracybase