Combining data sets for PCA

Question

[raalsuwaidi]

Hello

I have a local genome panel VCF file. I can use PLINK to transform it to the appropriate format and apply a PCA analysis.

But I want to perform the analysis comparatively between the local data set and the 1000 genome data. This means that I will combine the files and run the PCA command on the combined version.

Now will the plot show me which cluster belongs to which set? How can I do that?