The MAGMA SNP-wise models can also be used to analyse raw genotype data, in which case the raw genotype data takes the place of the reference data and the SNP p-values are computed internally. Gene-set analysis based on these SNP-wise models proceeds in the same way as the gene-set analysis based on the multiple regression gene analysis model. The gene p-values resulting from the analysis are converted to Z-values in the same way to serve as input for the gene-set analysis. Similarly, the gene-gene correlation matrix R is obtained using the same formula as with the multiple regression model, but using the reference data to compute it.
