Exploring a dataset with sgkit

In this recipe, we will perform an initial exploratory analysis of one of our generated datasets. Now that we have some basic knowledge of xarray, we can actually try to do some data analysis. In this recipe, we will ignore population structure, an issue we will return to in the following one.

Getting ready

You will need to have run the first recipe and should have the hapmap10_auto_noofs_ld files available. There is a Notebook file with this recipe called Chapter06/Exploratory_Analysis.py. You will need the software that you installed for the previous recipe.

How to do it...

Take a look at the following steps:

1. We start by loading the PLINK data with sgkit, exactly as in the previous recipe:

   import numpy as np
   import xarray as xr
   import sgkit as sg
   from sgkit.io import plink
    
   data = plink.read_plink(path='hapmap10_auto_noofs_ld', fam_sep='\t')

2. Let’s ask sgkit for variant_stats:

   variant_stats = sg.variant_stats...