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In [1]:

    
%matplotlib inline
from sr import cluster_data

# set up clustering for dataset
bed_fn = "data/mouse/alldata"
cluster_data(bed_fn)









    



Loading fam file data/mouse/alldata.fam
Loading bim file data/mouse/alldata.bim
indexing snps
bed file is open data/mouse/alldata.bed
using c-based plink parser

We can clearly see four large blocks, which should reflect four mouse strains, as well as many small blocks on the diagonal, which reflect the fine-grained family structure within this data set.