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Mahmoud's pemp implementation #196

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9 changes: 7 additions & 2 deletions pyprophet/stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -143,8 +143,13 @@ def pemp(stat, stat0):
m = len(stat)
m0 = len(stat0)

statc = np.concatenate((stat, stat0))
v = np.array([True] * m + [False] * m0)
# ------- originally (as in r implementation):
#statc = np.concatenate((stat, stat0))
#v = np.array([True] * m + [False] * m0)
# ------- switching the positions of Targets and decoys to avoid pi0 becoming negative, basically, decoys win ties making p values more conservative
statc = np.concatenate((stat0, stat))
v = np.array( [False] * m0 + [True] * m)

perm = np.argsort(-statc, kind="mergesort") # reversed sort, mergesort is stable
v = v[perm]

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