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Fix tools.dataTools.VAF_pc_cc bug #20

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Fix tools.dataTools.VAF_pc_cc bug #20

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6 changes: 3 additions & 3 deletions tools/dataTools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,13 +220,13 @@ def VAF_pc_cc (X: np.ndarray, C: np.ndarray, A: np.ndarray) -> np.ndarray:
`VAFs`: np.array with VAF for each axes of `C`, normalised between 0<VAF<1 for each axis, `sum(VAFs)` equals to total VAF.
"""
# following the notation in Gallego 2018
D = inv(A.T@A)@A.T@C
E = C.T@A
norm = lambda m:np.sum(m**2)

VAFs=np.empty((C.shape[0],))
for comp in range(1,C.shape[0]+1):
VAF = norm(X - X @ E[:,:comp] @ D[:comp,:]) / norm(X)
D = inv(A[:,:comp].T @ A[:,:comp]) @ A[:,:comp].T @ C
E = C.T @ A[:,:comp]
VAF = norm(X - X @ E @ D) / norm(X)
VAFs[comp-1] = 1-VAF

VAFs = np.array([VAFs[0],*np.diff(VAFs)])
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