regionsRanker.py 文件源码

def rankRegions(self, X, C, y, pos, regionLength, reml=True):

        #get resiong list
        regionsList = self.createRegionsList(pos, regionLength)

        #precompute log determinant of covariates
        XX = C.T.dot(C)
        [Sxx,Uxx]= la.eigh(XX)
        logdetXX  = np.log(Sxx).sum()

        #score each region
        betas = np.zeros(len(regionsList))
        for r_i, r in enumerate(regionsList):
            regionSize = len(r)

            if (self.verbose and r_i % 1000==0):
                print 'Testing region ' + str(r_i+1)+'/'+str(len(regionsList)),
                print 'with', regionSize, 'SNPs\t'

            s,U = self.eigenDecompose(X[:, np.array(r)], None)
            sig2g_kernel, sig2e_kernel, fixedEffects, ll = self.optSigma2(U, s, y, C, logdetXX, reml)
            betas[r_i] = ll

        return regionsList, betas


    ### this code is taken from the FastLMM package (see attached license)###