For PCA in nuclear families, Zhu et al. [2008] proposed a method for obtaining ancestry informative principal components (PCs) that performs a PCA using only the genotyped parents and then uses the weights of the SNPs from the PCA to obtain PCs for the offspring. Thornton et al. [2013] extended the Zhu et al. [2013] approach and developed the R-PCA method for ancestry informative PCA with general pedigrees. R-PCA performs a PCA using all pedigree founders who have SNP genotype data available so that the principal components are informative for ancestry. The SNP weights from the PCA with the pedigree founders are then used to compute PCs for all non-founders who are genotyped in the pedigree. The R-PCA method was applied to the GAW18 pedigrees, and the top principal components were compared to the top principal components from EIGENSTRAT and to global ancestry estimates from the previously described supervised ADMIXTURE analysis of Thornton et al. [2013].
