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RAISS
Commit eb8f3068 authored by Hanna JULIENNE's avatar Hanna JULIENNE
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Corrected causal simultation

parent 7b31ec08
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    Simulation/causal_example.html → Simulation/Causal_peaks_simulation.html
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    Simulation/Causal_peaks_simulation.ipynb
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    Simulation/causal_simulation.py
    View file @ eb8f3068
    ......@@ -28,10 +28,12 @@ def compute_Y(beta, X, sig=1.0):
    return Y
    def compute_Zscore(Y, X):
    nind = X.shape[0]
    Zscores = np.zeros(X.shape[1])
    for i in range(X.shape[1]):
    Zscores[i] = X.iloc[:,i].dot(Y) / X.iloc[:,i].dot(X.iloc[:,i])
    Zscores = (Zscores - Zscores.mean()) / np.std(Zscores)
    Zscores[i] = X.iloc[:,i].corr(Y)# X.iloc[:,i].dot(Y) / X.iloc[:,i].dot(X.iloc[:,i])
    Zscores = Zscores*nind**0.5
    #Zscores = (Zscores - Zscores.mean()) / np.std(Zscores)
    return Zscores
    def generate_one_causal(amplitude, LD_cor, X):
    ......@@ -76,7 +78,6 @@ def best_rd(zscore, LD_cor, ids_known, ids_masked):
    "rcond":np.argmax(cor_perf)})
    if __name__=="__main__":
    os.chdir("/home/hjulienn/Project/raiss/Simulation/")
    #get genotype
    X = pd.read_csv("./data/genotype.csv", sep="\t")
    nsnp = X.shape[1]
    ......@@ -89,11 +90,11 @@ if __name__=="__main__":
    ids_known = np.setdiff1d(np.array(range(100)), ids_masked)
    amplitude_effect = pd.Series(index=np.arange(0,50,1))
    tag = "one_positive"
    tag = "two_opposite"
    for amp in amplitude_effect.index:
    print('search of best rd for amplitude {}'.format(amp))
    signal = generate_one_causal(amp, LD_cor, X)
    signal = generate_two_opposite(amp, LD_cor, X)
    Zscore = signal["Zscore"]
    beta = signal["causal"]
    ......
    Simulation/results/Beta_one_positive.csv
    View file @ eb8f3068
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