The data frame contains two PCs. In this simulation example,we considered the 7 populations from African ancestry which were created from Phase 3 of 1000 Genomes, incorporating two populations from America continent and five populations from African continent. To derive the axes of genetic variation, in each reference panel, we used a subset of genetic variants with minor allele frequency (MAF) >5% in all populations, which were separated by 1Mb, to derive the matrix of pairwise Euclidean distances between the populations. Then the two axes of genetic variation would be derived from the multi-dimensional scaling of the distance matrix in the corresponding reference panel.
pcsAn object of class data.table (inherits from data.frame) with 7 rows and 2 columns.
7 populations of African ancestry were collected from Phase 3 of 1000 Genomes https://ctg.cncr.nl/software/MAGMA/ref_data/.