I did PCA analysis using pca function from the LEA r package
It produces these files:
eigenvalue file: genotypes_cultivated.eigenvalues
eigenvector file: genotypes_cultivated.eigenvectors
standard deviation file: genotypes_cultivated.sdev
projection file: genotypes_cultivated.projections
pcaProject file: genotypes_cultivated.pcaProject
From the projection file, I can plot the PC1 and PC2 ....
I wonder if there is a way to calculate the loadings of SNPs to the PC1 or PC2, in another word, I want to calculate the contribution of alleles to the first or second principal component of the PCA analysis.