PCA biplot for SNPs data

Question

[young_bioinformatician]

Hey guys,

Hope you all are well. It is just a quick and simple question but actually not simple for me :) I was wondering If I can draw a PCA population plot including individual and SNPs (directions).

I am using smartpca and there is no output file that contains this information to draw this kind of biplot and also was wondering what is exactly the differences between smartpca and prcomp ? Could I do same analysis using prcomp ?

Thanks a lot for the answers in advance.

[Hamid Ghaedi]

"prcomp" is a function from the base package "stat" todo principal component analysis (PCA), while smartpca is a program helping to run PCA on input genotype data. As indicated in the seminal paper in the smartpca another statical technique on top of PCA is used to detect population structure. So I would say for population genetic data structure identification you might stick to the smartpca.

[young_bioinformatician]

Thank you Hamid for clarifying the differences and yes, I just realized the point. To infer population structure, It makes sense. However, I can use classic PCA to separate individuals and their variables (SNPs) anyways, cannot I ? I have a bit unusual data,a lot of missings genotypes and also small amount of SNPs. So, I am not sure If smartpca is good for small dataset so I wanted to see classic PCA as well.