def compute_Kbg_excluded_chrom(self, chrom_i): """ computes the background covariance matrix from all SNPs that are not on chromosome chrom_i """ idx_bg = self.chrom != chrom_i M = self.M[idx_bg] Kbg = utils.computeLinearKernel(M.T) return Kbg
def compute_Kbg_excluded_chrom(self,chrom_i): """ computes the background covariance matrix from all SNPs that are not on chromosome chrom_i """ idx_bg = self.chrom!=chrom_i M = self.M[idx_bg] Kbg = utils.computeLinearKernel(M.T) return Kbg
def set_K(self,K=None, X=None, U=None, S=None): """ setting background covariance matrix input: K : covariance matrix [NxN] X : genetric markers used for constructing the covariance marix [NxF]. """ N = self.genoreader.get_ncols() if K is not None: assert K.shape[0]==N assert K.shape[1]==N self.K = K if X is not None: assert X.shape[0]==N self.K = utils.computeLinearKernel(X) if (U is None) or (S is None): S,U = scipy.linalg.eigh(K) self.S = S self.U = U
def set_K(self, K=None, X=None, U=None, S=None): """ setting background covariance matrix input: K : covariance matrix [NxN] X : genetric markers used for constructing the covariance marix [NxF]. """ N = self.genoreader.get_ncols() if K is not None: assert K.shape[0] == N assert K.shape[1] == N self.K = K if X is not None: assert X.shape[0] == N self.K = utils.computeLinearKernel(X) if (U is None) or (S is None): S, U = scipy.linalg.eigh(K) self.S = S self.U = U