def test_linreg(self): logging.info("TestSingleSnpLinReg test_linreg") test_snps = Bed(self.bedbase, count_A1=False) pheno = self.phen_fn covar = self.cov_fn output_file = self.file_name("linreg") frame1 = single_snp_linreg(test_snps=test_snps[:, :10], pheno=pheno, covar=covar, output_file_name=output_file, count_A1=False) frame1 = frame1[[ 'sid_index', 'SNP', 'Chr', 'GenDist', 'ChrPos', 'PValue' ]] self.compare_files(frame1, "linreg") frame2 = single_snp_linreg(test_snps=test_snps[:, :10], pheno=pheno, covar=covar, output_file_name=output_file, count_A1=False) self.compare_files(frame2, "linreg")
def test_linreg(self): logging.info("TestSingleSnp test_linreg") test_snps = Bed(self.bedbase) pheno = self.phen_fn covar = self.cov_fn output_file = self.file_name("linreg") frame1 = single_snp(test_snps=test_snps[:, :10], pheno=pheno, mixing=0, leave_out_one_chrom=False, G0=KernelIdentity(iid=test_snps.iid), covar=covar, output_file_name=output_file) frame1 = frame1[[ 'sid_index', 'SNP', 'Chr', 'GenDist', 'ChrPos', 'PValue' ]] self.compare_files(frame1, "linreg") frame2 = single_snp_linreg(test_snps=test_snps[:, :10], pheno=pheno, covar=covar, output_file_name=output_file) self.compare_files(frame2, "linreg")
def top_snps_for_each_fold_nested(kfold_item): fold_index, (train_idx, test_idx) = kfold_item _, G_in, pheno_in, covar_in = _fixup(test_snps, G, pheno, covar) nested = single_snp_linreg(G_in[train_idx, :], pheno_in[train_idx, :], covar_in[train_idx, :], GB_goal=GB_goal, max_output_len=max(k_list_in)) return nested
def test_linreg(self): logging.info("TestSingleSnpLinReg test_linreg") test_snps = Bed(self.bedbase) pheno = self.phen_fn covar = self.cov_fn output_file = self.file_name("linreg") frame1 = single_snp_linreg(test_snps=test_snps[:,:10], pheno=pheno, covar=covar, output_file_name=output_file ) frame1 = frame1[['sid_index', 'SNP', 'Chr', 'GenDist', 'ChrPos', 'PValue']] self.compare_files(frame1,"linreg") frame2 = single_snp_linreg(test_snps=test_snps[:,:10], pheno=pheno, covar=covar, output_file_name=output_file ) self.compare_files(frame2,"linreg")
def test_linreg(self): logging.info("TestSingleSnp test_linreg") test_snps = Bed(self.bedbase, count_A1=False) pheno = self.phen_fn covar = self.cov_fn output_file = self.file_name("linreg") frame1 = single_snp(test_snps=test_snps[:,:10], pheno=pheno, mixing=0,leave_out_one_chrom=False, G0=KernelIdentity(iid=test_snps.iid), covar=covar, output_file_name=output_file,count_A1=False ) frame1 = frame1[['sid_index', 'SNP', 'Chr', 'GenDist', 'ChrPos', 'PValue']] self.compare_files(frame1,"linreg") frame2 = single_snp_linreg(test_snps=test_snps[:,:10], pheno=pheno, covar=covar, output_file_name=output_file ) self.compare_files(frame2,"linreg")
def top_snps_for_each_fold_nested(kfold_item): fold_index, (train_idx, test_idx) = kfold_item _, G_in, pheno_in, covar_in = _fixup(test_snps, G, pheno, covar,count_A1=count_A1) nested = single_snp_linreg(G_in[train_idx,:],pheno_in[train_idx,:],covar_in[train_idx,:],GB_goal=GB_goal,max_output_len=max(k_list_in),count_A1=count_A1) return nested