Index

_

__call__() (deeprvat.metrics.AveragePrecisionWithLogits method) (deeprvat.metrics.PearsonCorr method) (deeprvat.metrics.PearsonCorrTorch method) (deeprvat.metrics.RSquared method)

__getitem__() (deeprvat.data.dense_gt.DenseGTDataset method) (deeprvat.deeprvat.train.MultiphenoDataset method) __len__() (deeprvat.data.dense_gt.DenseGTDataset method) (deeprvat.deeprvat.train.MultiphenoDataset method) _add_annotation_cols() (in module deeprvat.seed_gene_discovery.seed_gene_discovery)

A

ACTIVATIONS (in module deeprvat.deeprvat.train) add_gene_ids() (in module deeprvat.annotations.annotations) add_ids() (in module deeprvat.annotations.annotations) add_ids_dask() (in module deeprvat.annotations.annotations) add_variant_ids() (in module deeprvat.preprocessing.preprocess) AGG_FCT (in module deeprvat.deeprvat.associate) aggregate_abscores() (in module deeprvat.annotations.annotations)

aggregate_and_concat_absplice() (in module deeprvat.annotations.annotations) aggregate_pvals_per_gene() (in module deeprvat.deeprvat.evaluate) AGGREGATIONS (in module deeprvat.data.dense_gt) apply_thresholds() (deeprvat.data.rare.PaddedAnnotations method) (deeprvat.data.rare.SparseGenotype method) average_burdens() (in module deeprvat.deeprvat.associate) AveragePrecisionWithLogits (class in deeprvat.metrics)

B

BASELINE_GROUPS (in module deeprvat.deeprvat.evaluate) BaseModel (class in deeprvat.deeprvat.models)

best_training_run() (in module deeprvat.deeprvat.train) bfcorrect_df() (in module deeprvat.utils) BURDEN_SKAT_RENAME (in module deeprvat.deeprvat.evaluate)

C

calculate_beta_maf_weights() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) calculate_maf() (in module deeprvat.annotations.annotations) calculate_mean_std() (in module deeprvat.utils) calculate_pearsonr() (deeprvat.metrics.PearsonCorrTorch method) calculate_scores_max() (in module deeprvat.annotations.annotations) calculate_sift_polyphen_weights() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) call_score() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) center() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) chunks() (in module deeprvat.annotations.annotations) cli() (in module deeprvat.annotations.annotations) (in module deeprvat.cv_utils) (in module deeprvat.deeprvat.associate) (in module deeprvat.deeprvat.common_variant_condition_utils) (in module deeprvat.deeprvat.config) (in module deeprvat.deeprvat.train) (in module deeprvat.preprocessing.preprocess) (in module deeprvat.seed_gene_discovery.evaluate) (in module deeprvat.seed_gene_discovery.seed_gene_discovery) collapse_burden() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) collate_fn() (deeprvat.data.dense_gt.DenseGTDataset method) (deeprvat.data.rare.PaddedAnnotations method) (deeprvat.data.rare.SparseGenotype method) combine_burden_chunks() (in module deeprvat.deeprvat.associate) combine_burden_chunks_() (in module deeprvat.deeprvat.associate)

combine_genotypes() (in module deeprvat.preprocessing.preprocess) combine_regression_results() (in module deeprvat.deeprvat.associate) combine_results() (in module deeprvat.deeprvat.evaluate) (in module deeprvat.seed_gene_discovery.seed_gene_discovery) combine_test_set_burdens() (in module deeprvat.cv_utils) compression_level (in module deeprvat.deeprvat.common_variant_condition_utils) compute_burdens() (in module deeprvat.deeprvat.associate) compute_burdens_() (in module deeprvat.deeprvat.associate) compute_plof() (in module deeprvat.annotations.annotations) compute_se() (in module deeprvat.utils) compute_xy() (in module deeprvat.deeprvat.associate) compute_xy_() (in module deeprvat.deeprvat.associate) concat_annotations() (in module deeprvat.annotations.annotations) concatenate_deepsea() (in module deeprvat.annotations.annotations) configure_callbacks() (deeprvat.deeprvat.models.BaseModel method) configure_optimizers() (deeprvat.deeprvat.models.BaseModel method) convert2bed() (in module deeprvat.annotations.annotations) convert_regenie_output() (in module deeprvat.deeprvat.associate) convert_regenie_output_() (in module deeprvat.deeprvat.associate) copy_with_env() (in module deeprvat.utils) count_unique() (in module deeprvat.deeprvat.evaluate) create_gene_id_file() (in module deeprvat.annotations.annotations) create_main_config() (in module deeprvat.deeprvat.config) create_sg_discovery_config() (in module deeprvat.deeprvat.config)

D

DATA_SLOT_DICT (in module deeprvat.cv_utils) deepripe_encode_variant_bedline() (in module deeprvat.annotations.annotations) deepripe_get_model_info() (in module deeprvat.annotations.annotations) deepripe_score_variant_onlyseq_all() (in module deeprvat.annotations.annotations) deeprvat module deeprvat.annotations module deeprvat.annotations.annotations module deeprvat.cv_utils module deeprvat.data module deeprvat.data.dense_gt module deeprvat.data.rare module deeprvat.deeprvat module deeprvat.deeprvat.associate module deeprvat.deeprvat.common_variant_condition_utils module deeprvat.deeprvat.config module deeprvat.deeprvat.evaluate module

deeprvat.deeprvat.models module deeprvat.deeprvat.train module deeprvat.metrics module deeprvat.preprocessing module deeprvat.preprocessing.preprocess module deeprvat.seed_gene_discovery module deeprvat.seed_gene_discovery.evaluate module deeprvat.seed_gene_discovery.seed_gene_discovery module deeprvat.utils module deepsea_pca() (in module deeprvat.annotations.annotations) DeepSet (class in deeprvat.deeprvat.models) DeepSetAgg (class in deeprvat.deeprvat.models) DEFAULT_CHROMOSOMES (in module deeprvat.data.dense_gt) DEFAULT_OPTIMIZER (in module deeprvat.deeprvat.train) dense_to_sparse() (deeprvat.data.dense_gt.DenseGTDataset method) DenseGTDataset (class in deeprvat.data.dense_gt) drop_rows() (in module deeprvat.preprocessing.preprocess)

E

embed() (deeprvat.data.rare.PaddedAnnotations method) (deeprvat.data.rare.SparseGenotype method) evaluate() (in module deeprvat.deeprvat.evaluate) (in module deeprvat.seed_gene_discovery.evaluate)

evaluate_() (in module deeprvat.deeprvat.evaluate) (in module deeprvat.seed_gene_discovery.evaluate)

F

fdrcorrect_df() (in module deeprvat.utils) filter_annotations_by_exon_distance() (in module deeprvat.annotations.annotations) forward() (deeprvat.deeprvat.models.DeepSet method) (deeprvat.deeprvat.models.DeepSetAgg method) (deeprvat.deeprvat.models.LinearAgg method) (deeprvat.deeprvat.models.TwoLayer method)

G

generate_test_config() (in module deeprvat.cv_utils) get_af_from_gt() (in module deeprvat.annotations.annotations) get_anno() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) get_annotations() (deeprvat.data.dense_gt.DenseGTDataset method) get_baseline() (in module deeprvat.deeprvat.evaluate) get_baseline_results() (in module deeprvat.deeprvat.evaluate) get_burden() (in module deeprvat.deeprvat.associate) get_caf() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) get_common_variants() (deeprvat.data.dense_gt.DenseGTDataset method) get_file_chromosome() (in module deeprvat.preprocessing.preprocess) get_hparam() (in module deeprvat.deeprvat.models) get_matched_sample_indices() (in module deeprvat.data.dense_gt)

get_metadata() (deeprvat.data.dense_gt.DenseGTDataset method) (deeprvat.data.rare.PaddedAnnotations method) (deeprvat.data.rare.SparseGenotype method) get_parquet_columns() (in module deeprvat.annotations.annotations) get_pvals() (in module deeprvat.deeprvat.evaluate) get_rare_variants() (deeprvat.data.dense_gt.DenseGTDataset method) get_significant_genes() (in module deeprvat.deeprvat.common_variant_condition_utils) get_stand_params() (deeprvat.data.dense_gt.DenseGTDataset method) get_variant_groups() (deeprvat.data.dense_gt.DenseGTDataset method) get_variant_ids() (deeprvat.data.dense_gt.DenseGTDataset method) get_variant_metadata() (deeprvat.data.dense_gt.DenseGTDataset method) get_weights() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) GotNone

H

handle_cv_options() (in module deeprvat.deeprvat.config)

handle_pretrained_models() (in module deeprvat.deeprvat.config) handle_regenie_options() (in module deeprvat.deeprvat.config)

I

index_input_tensor_zarr() (deeprvat.deeprvat.train.MultiphenoDataset method)

L

LinearAgg (class in deeprvat.deeprvat.models) load_models() (in module deeprvat.deeprvat.associate) load_one_model() (in module deeprvat.deeprvat.associate) load_or_init() (in module deeprvat.utils) load_yaml() (in module deeprvat.deeprvat.config) logger (in module deeprvat.annotations.annotations) (in module deeprvat.cv_utils) (in module deeprvat.data.dense_gt) (in module deeprvat.data.rare) (in module deeprvat.deeprvat.associate) (in module deeprvat.deeprvat.common_variant_condition_utils) (in module deeprvat.deeprvat.config) (in module deeprvat.deeprvat.evaluate) (in module deeprvat.deeprvat.models) (in module deeprvat.deeprvat.train) (in module deeprvat.metrics) (in module deeprvat.preprocessing.preprocess) (in module deeprvat.seed_gene_discovery.evaluate) (in module deeprvat.seed_gene_discovery.seed_gene_discovery) (in module deeprvat.utils)

M

make_dataset() (in module deeprvat.deeprvat.associate) (in module deeprvat.deeprvat.train) (in module deeprvat.seed_gene_discovery.seed_gene_discovery) make_dataset_() (in module deeprvat.deeprvat.associate) (in module deeprvat.deeprvat.train) (in module deeprvat.seed_gene_discovery.seed_gene_discovery) make_regenie_input() (in module deeprvat.deeprvat.associate) make_regenie_input_() (in module deeprvat.deeprvat.associate) merge_abscores() (in module deeprvat.annotations.annotations) merge_absplice_scores() (in module deeprvat.annotations.annotations) merge_af() (in module deeprvat.annotations.annotations) merge_annotations() (in module deeprvat.annotations.annotations) merge_deepripe() (in module deeprvat.annotations.annotations) merge_deepsea_pcas() (in module deeprvat.annotations.annotations) METHOD_NAMES (in module deeprvat.deeprvat.evaluate) METRICS (in module deeprvat.deeprvat.models) (in module deeprvat.deeprvat.train) min_Bonferroni_aggregate() (in module deeprvat.deeprvat.evaluate) module deeprvat deeprvat.annotations deeprvat.annotations.annotations deeprvat.cv_utils deeprvat.data deeprvat.data.dense_gt deeprvat.data.rare deeprvat.deeprvat deeprvat.deeprvat.associate deeprvat.deeprvat.common_variant_condition_utils deeprvat.deeprvat.config deeprvat.deeprvat.evaluate deeprvat.deeprvat.models deeprvat.deeprvat.train deeprvat.metrics deeprvat.preprocessing deeprvat.preprocessing.preprocess deeprvat.seed_gene_discovery deeprvat.seed_gene_discovery.evaluate deeprvat.seed_gene_discovery.seed_gene_discovery deeprvat.utils

module_folder_dict (in module deeprvat.cv_utils) MultiphenoBaggingData (class in deeprvat.deeprvat.train) MultiphenoDataset (class in deeprvat.deeprvat.train) my_quantile_transform() (in module deeprvat.utils)

O

OPTIMIZERS (in module deeprvat.deeprvat.train)

P

PaddedAnnotations (class in deeprvat.data.rare) parse_file_path_list() (in module deeprvat.preprocessing.preprocess) PearsonCorr (class in deeprvat.metrics) PearsonCorrTorch (class in deeprvat.metrics) PLOF_COLS (in module deeprvat.deeprvat.associate) postprocess_sparse_gt() (in module deeprvat.preprocessing.preprocess) precision() (in module deeprvat.annotations.annotations) prepare_genotypes_per_gene() (in module deeprvat.deeprvat.common_variant_condition_utils)

process_chunk() (in module deeprvat.annotations.annotations) process_chunk_addids() (in module deeprvat.annotations.annotations) process_deepripe() (in module deeprvat.annotations.annotations) process_individual_missingness() (in module deeprvat.preprocessing.preprocess) process_results() (in module deeprvat.deeprvat.evaluate) process_sparse_gt() (in module deeprvat.preprocessing.preprocess) process_sparse_gt_file() (in module deeprvat.preprocessing.preprocess) process_vep() (in module deeprvat.annotations.annotations) pval_correction() (in module deeprvat.utils)

Q

qqplot() (in module deeprvat.seed_gene_discovery.evaluate)

R

ragged_to_matrix() (in module deeprvat.preprocessing.preprocess) read_deepripe_file() (in module deeprvat.annotations.annotations) readYamlColumns() (in module deeprvat.annotations.annotations) recall() (in module deeprvat.annotations.annotations) regress() (in module deeprvat.deeprvat.associate) regress_() (in module deeprvat.deeprvat.associate) regress_common() (in module deeprvat.deeprvat.associate) regress_common_() (in module deeprvat.deeprvat.associate) regress_on_gene() (in module deeprvat.deeprvat.associate) regress_on_gene_scoretest() (in module deeprvat.deeprvat.associate)

remap_group_ids() (deeprvat.data.rare.PaddedAnnotations method) (deeprvat.data.rare.SparseGenotype method) remove_prefix() (in module deeprvat.utils) replace_in_array() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) REPO_DIR (in module deeprvat.deeprvat.config) resolve_path_with_env() (in module deeprvat.utils) reverse_models() (in module deeprvat.deeprvat.associate) RSquared (class in deeprvat.metrics) run_association() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) run_association_() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) run_bagging() (in module deeprvat.deeprvat.train)

S

safe_merge() (in module deeprvat.utils) save_burdens() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) scorevariants_deepripe() (in module deeprvat.annotations.annotations) select_rename_fill_annotations() (in module deeprvat.annotations.annotations) separate_parallel_results() (in module deeprvat.deeprvat.associate) seq_to_1hot() (in module deeprvat.annotations.annotations) set_reverse() (deeprvat.deeprvat.models.DeepSetAgg method) (deeprvat.deeprvat.models.LinearAgg method) setup_annotations() (deeprvat.data.dense_gt.DenseGTDataset method) (deeprvat.data.rare.PaddedAnnotations method) (deeprvat.data.rare.SparseGenotype method) setup_common_groups() (deeprvat.data.dense_gt.DenseGTDataset method) setup_logging() (in module deeprvat.deeprvat.config)

setup_metadata() (deeprvat.data.rare.PaddedAnnotations method) (deeprvat.data.rare.SparseGenotype method) setup_phenotypes() (deeprvat.data.dense_gt.DenseGTDataset method) setup_variants() (deeprvat.data.dense_gt.DenseGTDataset method) setup_zarr() (deeprvat.data.dense_gt.DenseGTDataset method) SparseGenotype (class in deeprvat.data.rare) spread_config() (in module deeprvat.cv_utils) standardize_series() (in module deeprvat.utils) standardize_series_with_params() (in module deeprvat.utils) subset_matrix() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) subset_samples() (in module deeprvat.deeprvat.train) suggest_batch_size() (in module deeprvat.utils) suggest_hparams() (in module deeprvat.utils)

T

test_epoch_end() (deeprvat.deeprvat.models.BaseModel method) test_gene() (in module deeprvat.seed_gene_discovery.seed_gene_discovery) test_step() (deeprvat.deeprvat.models.BaseModel method) train() (in module deeprvat.deeprvat.train)

train_dataloader() (deeprvat.deeprvat.train.MultiphenoBaggingData method) training_step() (deeprvat.deeprvat.models.BaseModel method) transform_data() (deeprvat.data.dense_gt.DenseGTDataset method) TwoLayer (class in deeprvat.deeprvat.models)

U

update_config() (in module deeprvat.deeprvat.config) (in module deeprvat.seed_gene_discovery.seed_gene_discovery) update_defaults() (in module deeprvat.deeprvat.config)

update_full_config() (in module deeprvat.deeprvat.config) update_thresholds() (in module deeprvat.deeprvat.config) upsample() (deeprvat.deeprvat.train.MultiphenoBaggingData method)

V

val_dataloader() (deeprvat.deeprvat.train.MultiphenoBaggingData method) validate_keys() (in module deeprvat.deeprvat.config) validation_epoch_end() (deeprvat.deeprvat.models.BaseModel method)

validation_step() (deeprvat.deeprvat.models.BaseModel method) VARIANT_TYPE_RENAME (in module deeprvat.deeprvat.evaluate) variant_weight_th_dict (in module deeprvat.seed_gene_discovery.seed_gene_discovery)

W

write_genotype_file() (in module deeprvat.preprocessing.preprocess)