GWAS2 : GWAA; New Data Generation« Back to Modules List
TitleGWAA; New Data Generation
AuthorSara Nunez, Tu Dao
DescriptionNew data generation is the second step involved in many GWAS analyses. It involves generating principal components to be included in a predictive model as well as imputing missing SNPs to increase power. Work saved from module 1 in this series (entitled GWAS1) is utilizing in these labs. The first lab in this module walks students through how to compute principal components (PCs) to be used in a model of association. This is done to adjust for population substructure in the data. The second lab demonstrates one way that missing SNPs can be imputed using a reference panel. In our example, we impute SNPs that are present in the 1000 Genomes Project data on chromosome 16. In practice, this can be done in R but is more commonly done using external tools.