diff options
| -rw-r--r-- | gn3/computations/partial_correlations.py | 55 | ||||
| -rw-r--r-- | gn3/db/partial_correlations.py | 2 |
2 files changed, 55 insertions, 2 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index f82031a..0041684 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -19,8 +19,8 @@ from gn3.settings import TEXTDIR from gn3.random import random_string from gn3.function_helpers import compose from gn3.data_helpers import parse_csv_line -from gn3.db.traits import export_informative from gn3.db.datasets import retrieve_trait_dataset +from gn3.db.traits import export_trait_data, export_informative from gn3.db.partial_correlations import traits_info, traits_data from gn3.db.species import species_name, translate_to_mouse_gene_id from gn3.db.correlations import ( @@ -807,3 +807,56 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] "dataset_type": target_dataset["type"], "method": "spearman" if "spearman" in method.lower() else "pearson" }} + + +def partial_correlations_with_target_traits( + conn: Any, primary_trait_name: str, + control_trait_names: Tuple[str, ...], + target_trait_names: Tuple[str, ...], method: str) -> dict: + """ + Compute partial correlation against a specific selection of traits. + """ + threshold = 0 + check_res = check_for_common_errors( + conn, primary_trait_name, control_trait_names) + if check_res.get("status") == "error": + return error_check_results + + target_traits = { + trait["name"]: trait + for trait in traits_info(conn, threshold, target_trait_names)} + target_traits_data = traits_data(conn, target_traits.values()) + + def __merge(trait, pcorrs): + return { + **trait, + "noverlap": pcorrs[1], + "partial_corr": pcorrs[2], + "partial_corr_p_value": pcorrs[3], + "corr": pcorrs[4], + "corr_p_value": pcorrs[5]} + + all_pcorrs = ( + __merge( + target_traits[target_name], + compute_trait_info( + check_res["primary_values"], check_res["fixed_control_values"], + (export_trait_data( + target_data, + samplelist=check_res["common_primary_control_samples"]), + target_name), + method)) + for target_name, target_data in target_traits_data.items()) + + return { + "status": "success", + "results": { + "primary_trait": trait_for_output(check_res["primary_trait"]), + "control_traits": tuple( + trait_for_output(trait) for trait in + check_res["control_traits"]), + "correlations": tuple( + trait_for_output(trait) for trait in all_pcorrs), + "dataset_type": "NOT SET YET", + "method": "spearman" if "spearman" in method.lower() else "pearson" + }} diff --git a/gn3/db/partial_correlations.py b/gn3/db/partial_correlations.py index 72dbf1a..96f953d 100644 --- a/gn3/db/partial_correlations.py +++ b/gn3/db/partial_correlations.py @@ -783,7 +783,7 @@ def traits_info( partial(temp_traits_info, conn), partial(temp_traits_datasets, conn, threshold)) } - return tuple( + return ( trait for sublist in (# type: ignore[var-annotated] traits_fns[dataset_type](traits) for dataset_type, traits |