pleiopred_main.py 文件源码

def annopred_inf(beta_hats, pr_sigi, n=1000, reference_ld_mats=None, ld_window_size=100):
    """
    infinitesimal model with snp-specific heritability derived from annotation
    used as the initial values for MCMC of non-infinitesimal model
    """
    num_betas = len(beta_hats)
    updated_betas = sp.empty(num_betas)
    m = len(beta_hats)

    for i, wi in enumerate(range(0, num_betas, ld_window_size)):
        start_i = wi
        stop_i = min(num_betas, wi + ld_window_size)
        curr_window_size = stop_i - start_i
        Li = 1.0/pr_sigi[start_i: stop_i]
        D = reference_ld_mats[i]
        A = (n/(1))*D + sp.diag(Li)
        A_inv = linalg.pinv(A)
        updated_betas[start_i: stop_i] = sp.dot(A_inv / (1.0/n) , beta_hats[start_i: stop_i])  # Adjust the beta_hats

    return updated_betas