github.com/PRIMED-Ancestry-Inference/PCA_projection/projected_PCA

run_projected_pca

This workflow is used to project a genetic test dataset (in plink format, i.e., .bed/.bim/.fam) into pca space using user-defined allele loadings. First, the allele loadings (.P produced by ADMIXTURE) and the test dataset are both subset to contain the same set of variants (Note: this workflow assumes that variants from both the loadings and test dataset have been previously harmonized such that variants follow the same naming convention, alleles at each site are ordered id


This is a companion discussion topic for the original entry at github.com/PRIMED-Ancestry-Inference/PCA_projection/projected_PCA