Question: How to check how much loading each SNP had on the first or second principal component
1
gravatar for Hann
12 months ago by
Hann80
KAUST
Hann80 wrote:

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.

snp pca • 443 views
ADD COMMENTlink modified 12 months ago by chrchang5237.4k • written 12 months ago by Hann80
1
gravatar for chrchang523
12 months ago by
chrchang5237.4k
United States
chrchang5237.4k wrote:

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

ADD COMMENTlink written 12 months ago by chrchang5237.4k

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

ADD REPLYlink written 12 months ago by Hann80
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