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Updated README for Clarity on Params #26

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Updated README for Clarity on Params #26

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7 changes: 6 additions & 1 deletion README.md
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Expand Up @@ -31,19 +31,24 @@ data = np.genfromtxt('testdata/testdata.csv', delimiter=",", skip_header=1)

# Specifying the batch (scanner variable) as well as a biological covariate to preserve:
covars = {'batch':[1,1,1,1,1,2,2,2,2,2],
'gender':[1,2,1,2,1,2,1,2,1,2]}
'gender':[1,2,1,2,1,2,1,2,1,2],
'age': [30, 20, 19, 21, 23, 30, 20, 19, 21, 23]}
covars = pd.DataFrame(covars)

# To specify names of the variables that are categorical:
categorical_cols = ['gender']

# To specify names of the variables that are continuous:
continuous_cols = ['age']

# To specify the name of the variable that encodes for the scanner/batch covariate:
batch_col = 'batch'

#Harmonization step:
data_combat = neuroCombat(dat=data,
covars=covars,
batch_col=batch_col,
continuous_cols=continuous_cols,
categorical_cols=categorical_cols)["data"]
```

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