diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 14 |
1 files changed, 10 insertions, 4 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 9bad12a..4b35c51 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -406,6 +406,12 @@ def partial_corrs(# pylint: disable=[R0913] `web.webqtl.correlation.PartialCorrDBPage.__init__` function in GeneNetwork1. """ + symbol_corr_dict, symbol_p_value_dict = correlations_of_all_tissue_traits( + fetch_gene_symbol_tissue_value_dict_for_trait( + (input_trait_symbol,), tissue_probeset_freeze_id, conn), + fetch_gene_symbol_tissue_value_dict_for_trait( + tuple(), tissue_probeset_freeze_id, conn), + method) if database_filename: return partial_correlations_fast( samples, primary_vals, control_vals, database_filename, @@ -414,15 +420,15 @@ def partial_corrs(# pylint: disable=[R0913] species, input_trait_geneid, dataset, return_number, conn) if "literature" in method.lower() else fetch_tissue_correlations( - dataset, input_trait_symbol, tissue_probeset_freeze_id, - method, return_number, conn)), + dataset, symbol_corr_dict, symbol_p_value_dict, + return_number, conn)), method, ("literature" if method.lower() == "sgo literature correlation" else ("tissue" if "tissue" in method.lower() else "genetic"))) trait_database, data_start_pos = fetch_all_database_data( - conn, species, input_trait_geneid, input_trait_symbol, samples, dataset, - method, return_number, tissue_probeset_freeze_id) + conn, species, input_trait_geneid, samples, dataset, method, + symbol_corr_dict, symbol_p_value_dict, return_number) return partial_correlations_normal( primary_vals, control_vals, input_trait_geneid, trait_database, data_start_pos, dataset, method) |