Index

_

__init__() (biomedical_data_generator.BatchEffectsConfig method) (biomedical_data_generator.ClassConfig method) (biomedical_data_generator.config.BatchEffectsConfig method) (biomedical_data_generator.config.ClassConfig method) (biomedical_data_generator.config.CorrClusterConfig method) (biomedical_data_generator.config.DatasetConfig method) (biomedical_data_generator.CorrClusterConfig method) (biomedical_data_generator.DatasetConfig method) (biomedical_data_generator.meta.DatasetMeta method)

A

apply_anchor_effects() (in module biomedical_data_generator.features.correlated) apply_batch_effects() (in module biomedical_data_generator.effects.batch)

apply_batch_effects_from_config() (in module biomedical_data_generator.effects.batch) assess_correlation_quality() (in module biomedical_data_generator.utils.correlation_tools)

B

BatchEffectsConfig (class in biomedical_data_generator) (class in biomedical_data_generator.config) biomedical_data_generator.effects.batch module biomedical_data_generator.features.correlated module biomedical_data_generator.features.informative module biomedical_data_generator.utils.correlation_tools module

biomedical_data_generator.utils.export_utils module biomedical_data_generator.utils.sklearn_compat module biomedical_data_generator.utils.visualization module breakdown() (biomedical_data_generator.config.DatasetConfig method), [1] (biomedical_data_generator.DatasetConfig method), [1] build_correlation_matrix() (in module biomedical_data_generator.features.correlated)

C

class_counts (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) class_labels (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) ClassConfig (class in biomedical_data_generator) (class in biomedical_data_generator.config) compute_correlation_matrix() (in module biomedical_data_generator.utils.correlation_tools) compute_correlation_matrix_for_cluster() (in module biomedical_data_generator.utils.correlation_tools)

compute_correlation_metrics() (in module biomedical_data_generator.utils.correlation_tools) confounded_batch_assignment() (in module biomedical_data_generator.effects.batch) CorrClusterConfig (class in biomedical_data_generator) (class in biomedical_data_generator.config) count_informative_anchors() (biomedical_data_generator.config.DatasetConfig method), [1] (biomedical_data_generator.DatasetConfig method), [1] count_noise_anchors() (biomedical_data_generator.config.DatasetConfig method), [1] (biomedical_data_generator.DatasetConfig method), [1]

D

DatasetConfig (class in biomedical_data_generator) (class in biomedical_data_generator.config)

DatasetMeta (class in biomedical_data_generator.meta)

F

find_best_seed_for_correlation() (in module biomedical_data_generator.utils.correlation_tools) find_seed_for_correlation() (in module biomedical_data_generator.utils.correlation_tools)

from_yaml() (biomedical_data_generator.config.DatasetConfig class method) (biomedical_data_generator.DatasetConfig class method)

G

generate_batch_assignments() (in module biomedical_data_generator.effects.batch) generate_dataset() (in module biomedical_data_generator) generate_informative_features() (in module biomedical_data_generator.features.informative)

get_cluster_column_names() (in module biomedical_data_generator.utils.correlation_tools) get_cluster_frame() (in module biomedical_data_generator.utils.correlation_tools) get_correlation_for_class() (biomedical_data_generator.config.CorrClusterConfig method) (biomedical_data_generator.CorrClusterConfig method)

I

is_class_specific() (biomedical_data_generator.config.CorrClusterConfig method) (biomedical_data_generator.CorrClusterConfig method)

M

make_biomedical_dataset() (in module biomedical_data_generator.utils.sklearn_compat) model_config (biomedical_data_generator.BatchEffectsConfig attribute) (biomedical_data_generator.ClassConfig attribute) (biomedical_data_generator.config.BatchEffectsConfig attribute) (biomedical_data_generator.config.ClassConfig attribute) (biomedical_data_generator.config.CorrClusterConfig attribute) (biomedical_data_generator.config.DatasetConfig attribute) (biomedical_data_generator.CorrClusterConfig attribute) (biomedical_data_generator.DatasetConfig attribute)

module biomedical_data_generator.effects.batch biomedical_data_generator.features.correlated biomedical_data_generator.features.informative biomedical_data_generator.utils.correlation_tools biomedical_data_generator.utils.export_utils biomedical_data_generator.utils.sklearn_compat biomedical_data_generator.utils.visualization

N

n_classes (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) n_features (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) n_informative_free (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property)

n_noise_free (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property) n_samples (biomedical_data_generator.config.DatasetConfig property) (biomedical_data_generator.DatasetConfig property)

P

parse_cluster_id() (in module biomedical_data_generator.utils.correlation_tools) pc1_share() (in module biomedical_data_generator.utils.correlation_tools) pc1_share_from_corr() (in module biomedical_data_generator.utils.correlation_tools)

plot_all_correlation_clusters() (in module biomedical_data_generator.utils.visualization) plot_correlation_matrices_per_cluster() (in module biomedical_data_generator.utils.visualization) plot_correlation_matrix() (in module biomedical_data_generator.utils.visualization) plot_correlation_matrix_for_cluster() (in module biomedical_data_generator.utils.visualization)

R

random_batch_assignment() (in module biomedical_data_generator.effects.batch)

resolve_anchor_effect_size() (biomedical_data_generator.config.CorrClusterConfig method) (biomedical_data_generator.CorrClusterConfig method)

S

sample_all_correlated_clusters() (in module biomedical_data_generator.features.correlated)

sample_correlated_data() (in module biomedical_data_generator.features.correlated)

T

to_csv() (in module biomedical_data_generator.utils.export_utils) to_dict() (biomedical_data_generator.meta.DatasetMeta method)

to_labeled_dataframe() (in module biomedical_data_generator.utils.export_utils) to_parquet() (in module biomedical_data_generator.utils.export_utils)

V

validate_proportions() (biomedical_data_generator.BatchEffectsConfig class method) (biomedical_data_generator.config.BatchEffectsConfig class method)

variance_partition_pc1() (in module biomedical_data_generator.utils.correlation_tools)