def get_qFDR(p): """Calculate the q-values using FDR correction""" n = len(p) q = np.zeros((n,n)) for i in range(n): tmp = p[i] # hide the element refereing to i,i comparision tmp[i]=np.nan _,qTmp,_ = statsUtil.fdr_bh(tmp) q[i] = qTmp return(q)
def getImpInfo(outDir, labels, name="fullACEImpResults.dat"):
"""Get the importance scores, the p-values and the q-values
for the importance score run results in indicated outDir.
Scores are returned in the same order as labels."""
# get data
impPath = outDir + "/" + name
data = np.loadtxt(impPath, dtype=str, delimiter="\t")
pTmp = np.array(data[:, 2], dtype=float)
impTmp = np.array(data[:, 3], dtype=float)
labelsTmp = data[:, 1]
# arrange data
_, qTmp, _ = statsUtil.fdr_bh(pTmp)
# rearange
n = len(labels)
p = np.zeros(n) + np.nan
q = np.zeros(n) + np.nan
imp = np.zeros(n) + np.nan
m = len(labelsTmp)
for i in range(m):
p[labels == labelsTmp[i]] = pTmp[i]
q[labels == labelsTmp[i]] = qTmp[i]
imp[labels == labelsTmp[i]] = impTmp[i]
return (imp, p, q)
