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gilesc/deseq_test_for_hunter.py

Created July 6, 2021 19:47
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deseq_test_for_hunter.py
import pandas as pd
import numpy as np
import patsy
import wrenlab.R.wrap.DESeq2
def fn():
X = pd.DataFrame(np.random.randint(10000, size=(12, 1000)))
D = pd.DataFrame({
"V1": [0,0,0,0,0,0,1,1,1,1,1,1],
"V2": [0,1,0,1,0,1,0,1,0,1,0,1]
})
D = patsy.dmatrix("V1 + V2 + V1:V2", D, return_type="dataframe")
return wrenlab.R.wrap.DESeq2.fit(D,X,"V1")
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