PLINK PCA Tutorial: Running PCA in PLINK (Commands + Output)
In this post, I’ll demonstrate how to perform a PCA on a PLINK dataset. Before we begin, we need to prepare a subset of samples we’re interested in analyzing. To do this, we’ll extract sample information from the .fam file. But first, we need to identify the samples of interest. For example, those from a specific population such as Sardinians. The easiest way is to open the corresponding .ind file and look at the population column, which is the third column in each row. Open the file in a text editor, and search for the population name, in this case, Sardinian. ...