PCA axis description SNPRelate
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serpalma.v ▴ 60
@serpalmav-8912
Last seen 4 months ago
Germany

Hello,

in the vignette for SNPRelate, under PCA, the plot is labeled as x="eigenvector 2" and y="eigenvector 1". My knowloedge on PCA is very basic and I was wondering if this is the same as x="PC2" and y="PC1".

Similarly, I want to also ask if the element $eigenvect in the pca object created by the function snpgdsPCA correspond to the loadings for each SNP.

As I said, my knowledge on PCA is very basic (I am working on it though) and apologize for this basic question.

SNPRelate PCA • 306 views
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@stephanie-m-gogarten-5121
Last seen 6 weeks ago
University of Washington

Yes, "principal component (PC)" and "eigenvector" mean the same thing. The element $eigenvect has the sample eigenvectors (each row corresponds to a sample). To obtain the SNP loadings, use the function snpgdsPCASNPLoading.

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