Question: PCA from genotype data using the --pca option in plink2
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gravatar for  DataFanatic
2.7 years ago by
DataFanatic260
DataFanatic260 wrote:

Hi, When computing PCA from genotype data using the --pca option in plink2, 1.Is it possible and more convenient to use data from one chromosome for the analysis? 2. Should my genotypes be LD pruned r<0.02? Thanks!

ld pruning pca plink2 • 1.1k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by DataFanatic260

I believe that it is only done per chromosome in the interest of saving RAM. You can very easily do PCA on the entire dateset, too.

Regarding LD pruning, it depends on what your end goals are.

ADD REPLYlink written 2.7 years ago by regmkbl66k
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