def make_table(model, gene):
table = summary_table(model)
# annotate table
if table.shape[0] > 0:
v2r = load_var2rsid(gene)
table.loc[:, 'rsid'] = table.variant_id.apply(lambda x: v2r.get(x, '-'))
table.loc[:, 'chr'] = table.variant_id.apply(lambda x: (x.split('_')[0]))
table.loc[:, 'start'] = table.variant_id.apply(lambda x: int(x.split('_')[1]))
table.loc[:, 'end'] = table.start + 1
table.loc[:, 'gene'] = gene
table = table.loc[:, ['chr', 'start', 'end', 'variant_id', 'rsid', 'study', 'pip', 'top_component', 'p_active', 'pi', 'alpha', 'rank', 'effect', 'effect_var']]
return table
def make_table(model, gene, rsid2variant_id):
table = summary_table(model)
# annotate table
table.loc[:, 'rsid'] = table.variant_id
table.loc[:, 'variant_id'] = table.rsid.apply(lambda x: rsid2variant_id.get(x, 'chr0_0_A_B_n'))
table.loc[:, 'chr'] = table.variant_id.apply(lambda x: (x.split('_')[0]))
table.loc[:, 'start'] = table.variant_id.apply(lambda x: int(x.split('_')[1]))
table.loc[:, 'end'] = table.start + 1
table.loc[:, 'gene'] = gene
table = table.loc[:, ['chr', 'start', 'end', 'gene',
'variant_id', 'rsid', 'study', 'pip',
'top_component', 'p_active', 'pi', 'alpha',
'rank', 'effect', 'effect_var']]
return table
'LD': sample_ld(gtex_genotype.loc[:, variants]),
'B': B,
'S': S,
'K': K,
'snp_ids': variants,
'study_ids': studies,
'tolerance': 1e-8
}
css = CSS(**init_args)
css.prior_activity = np.ones(K) * 0.1
css.weight_precision_b = np.ones_like(css.weight_precision_b) * 10
weight_ard_active_fit_procedure(css, max_iter=10, verbose=True)
fit_all(css, max_iter=30, verbose=True)
table = summary_table(css)
tables.append(table)
coloc_table.append(c(css, study=study, gene=gene, phenotye=phenotype, tissue=tissue))
# format results
table = pd.concat(tables)
table.loc[:, 'rsid'] = table.variant_id
table.loc[:, 'variant_id'] = table.rsid.apply(lambda x: rsid2variant_id.get(x))
table.loc[:, 'chr'] = table.variant_id.apply(lambda x: (x.split('_')[0]))
table.loc[:, 'start'] = table.variant_id.apply(lambda x: int(x.split('_')[1]))
table.loc[:, 'end'] = table.start + 1
table.loc[:, 'gene'] = gene
table = table.loc[:, [
'chr', 'start', 'end', 'gene', 'variant_id',
'rsid', 'study', 'pip', 'top_component',
'p_active', 'pi', 'alpha', 'rank', 'effect', 'effect_var']]