In this recipe, we'll look at constructing the data structures we need to run the analysis from input VCF files. We'll use the GWAS() function in the rrBLUP package. Our sample data file contains three SNPs—for didactic purposes, this will aid our programming task but for a GWAS study, the number is laughably small. Although the code will work, the results will not be biologically meaningful. 

We'll need rrBLUP, which is not part of Bioconductor, so install it with install.packages(), VariantAnnotation, and the datasets/ch2/small_sample.vcf file.