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AbdoNumen
12-08-2018, 03:38 AM
So I decided to dive into the world of R, without any prior experience. I'm fascinated by data analysis, visualization and genetics so I thought it'd be fun.

I followed a tutorial posted by Razib Khan in his blog last July, but lost him already on the first step (great start!). I installed Ubuntu, R and Rstudio, then installed the PLINK package and enabled it. Also downloaded the zip file with the reference data.

When he says the following, where does he mean us to input the "less"? In the linux terminal, R or elsewhere?


If you look in the “family” file you will see an important part of the structure. So do:

less Est1000HGDP.fam


https://www.gnxp.com/WordPress/2018/07/11/tutorial-to-run-pca-admixture-treemix-and-pairwise-fst-in-one-command/

If anyone has a step-by-step tutorial on how to create PCA plots with publicly available data and genotyped data from the major companies I'd really appreciate it.