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
