6.13 Performing PCA
We perform PCA on our genotype matrix with prcomp.
pca <- prcomp(gt_matrix_T)Our output is a prcomp object. This object comprises several tables, which you can preview by typing pca$ into the console and seeing what R suggests:
sdev: standard deviations of the principle componentsrotation,center,scale: tables we won’t use in this labx: coordinates of the data objects (the 1000 Genomes individuals) on each PC