Perform PCA

Question

[uhbyhh]

Hey , i have a ped file. How can i sue the ped file to perform PCA in ubuntu terminal using plink

Answer 1

[bk11]

Since you have .ped/.map file, you can perform PCA analysis using the following command-

plink --file your_plink_data --pca 10 --out your_plink_data_PCA 

Also you can convert your .ped/.map files into plink binary files .bed/.bim/.fam first and then run --pca as follows-

plink --file your_plink_data --make-bed --out your_plink_data_binary
plink --bfile your_plink_data_binary --pca 10 --out your_plink_data_binary_PCA