:py:mod:`deeprvat.seed_gene_discovery.seed_gene_discovery` ========================================================== .. py:module:: deeprvat.seed_gene_discovery.seed_gene_discovery .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery :allowtitles: Module Contents --------------- Functions ~~~~~~~~~ .. list-table:: :class: autosummary longtable :align: left * - :py:obj:`replace_in_array ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.replace_in_array :summary: * - :py:obj:`get_caf ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.get_caf :summary: * - :py:obj:`save_burdens ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.save_burdens :summary: * - :py:obj:`subset_matrix ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.subset_matrix :summary: * - :py:obj:`center ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.center :summary: * - :py:obj:`collapse_burden ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.collapse_burden :summary: * - :py:obj:`get_weights ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.get_weights :summary: * - :py:obj:`calculate_beta_maf_weights ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.calculate_beta_maf_weights :summary: * - :py:obj:`calculate_sift_polyphen_weights ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.calculate_sift_polyphen_weights :summary: * - :py:obj:`get_anno ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.get_anno :summary: * - :py:obj:`call_score ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.call_score :summary: * - :py:obj:`test_gene ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.test_gene :summary: * - :py:obj:`run_association_ ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.run_association_ :summary: * - :py:obj:`cli ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.cli :summary: * - :py:obj:`_add_annotation_cols ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery._add_annotation_cols :summary: * - :py:obj:`update_config ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.update_config :summary: * - :py:obj:`make_dataset_ ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.make_dataset_ :summary: * - :py:obj:`make_dataset ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.make_dataset :summary: * - :py:obj:`run_association ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.run_association :summary: * - :py:obj:`combine_results ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.combine_results :summary: Data ~~~~ .. list-table:: :class: autosummary longtable :align: left * - :py:obj:`logger ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.logger :summary: * - :py:obj:`variant_weight_th_dict ` - .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.variant_weight_th_dict :summary: API ~~~ .. py:data:: logger :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.logger :value: 'getLogger(...)' .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.logger .. py:data:: variant_weight_th_dict :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.variant_weight_th_dict :value: None .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.variant_weight_th_dict .. py:exception:: GotNone() :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.GotNone Bases: :py:obj:`Exception` .. py:function:: replace_in_array(arr, old_val, new_val) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.replace_in_array .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.replace_in_array .. py:function:: get_caf(G) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.get_caf .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.get_caf .. py:function:: save_burdens(GW_list, GW_full_list, split, chunk, out_dir) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.save_burdens .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.save_burdens .. py:function:: subset_matrix(M: typing.Any, train_proportion: int) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.subset_matrix .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.subset_matrix .. py:function:: center(X, inplace=False) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.center .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.center .. py:function:: collapse_burden(X, method='max') :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.collapse_burden .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.collapse_burden .. py:function:: get_weights(variant_ids, annotation_df, weight_cols, var_weight_function, maf_col) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.get_weights .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.get_weights .. py:function:: calculate_beta_maf_weights(anno, maf_col, beta_weights=(1, 25)) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.calculate_beta_maf_weights .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.calculate_beta_maf_weights .. py:function:: calculate_sift_polyphen_weights(anno) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.calculate_sift_polyphen_weights .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.calculate_sift_polyphen_weights .. py:function:: get_anno(G: numpy.ndarray, variant_ids: numpy.ndarray, annotation_df: pandas.DataFrame, weight_cols: typing.List[str], var_weight_function: str, maf_col: str) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.get_anno .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.get_anno .. py:function:: call_score(GV, null_model_score, pval_dict, test_type) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.call_score .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.call_score .. py:function:: test_gene(G_full: scipy.sparse.spmatrix, gene: int, grouped_annotations: pandas.DataFrame, Y, weight_cols: typing.List[str], null_model_score: seak.scoretest.ScoretestNoK, test_config: typing.Dict, var_type, test_type, maf_col, min_mac) -> typing.Dict[str, typing.Any] :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.test_gene .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.test_gene .. py:function:: run_association_(Y: numpy.ndarray, X: numpy.ndarray, gene_ids, G_full, grouped_annotations: pandas.DataFrame, dataset: deeprvat.data.DenseGTDataset, config: typing.Dict[str, typing.Any], var_type: str, test_type: str, persist_burdens: bool) -> pandas.DataFrame :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.run_association_ .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.run_association_ .. py:function:: cli() :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.cli .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.cli .. py:function:: _add_annotation_cols(annotations, config) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery._add_annotation_cols .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery._add_annotation_cols .. py:function:: update_config(old_config_file: str, phenotype: typing.Optional[str], simulated_phenotype_file: str, variant_type: typing.Optional[str], rare_maf: typing.Optional[float], maf_column: str, new_config_file: str) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.update_config .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.update_config .. py:function:: make_dataset_(config: typing.Dict, pickled_dataset_file: str = None, debug: bool = False, data_key='data') -> torch.utils.data.Dataset :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.make_dataset_ .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.make_dataset_ .. py:function:: make_dataset(debug: bool, data_key: str, config_file: str, pickled_dataset_file: str, out_file: str) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.make_dataset .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.make_dataset .. py:function:: run_association(debug: bool, dataset_file: typing.Optional[deeprvat.data.DenseGTDataset], data_file: typing.Optional[deeprvat.data.DenseGTDataset], config_file: str, var_type: str, test_type: str, out_path: str, persist_burdens: bool, n_chunks: typing.Optional[int] = None, chunk: typing.Optional[int] = None) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.run_association .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.run_association .. py:function:: combine_results(result_files: typing.Tuple[str], out_file: str) :canonical: deeprvat.seed_gene_discovery.seed_gene_discovery.combine_results .. autodoc2-docstring:: deeprvat.seed_gene_discovery.seed_gene_discovery.combine_results