How to check how much loading each SNP had on the first or second principal component

Question

[Hann]

Hello,

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.

Answer 1

[chrchang523]

With plink, —pca var-wts reports SNP loadings.

[Hann]

Thanks a lot! I know it's possible with plink and adegenet R package But because my PCA was produced by the pca function from the R package LEA. Then I would look for the loadings using the produced files by this function