Index

_

__init__() (pyproteonet.data.dataset.Dataset method) (pyproteonet.data.dataset.DatasetMoleculeValues method) (pyproteonet.data.dataset_sample.DatasetSample method) (pyproteonet.data.molecule_set.MoleculeMapping method) (pyproteonet.data.molecule_set.MoleculeSet method) (pyproteonet.imputation.dnn.gnn.heterogeneous.ImputationModule method) (pyproteonet.imputation.dnn.gnn.homogeneous.UncertaintyGAT method) (pyproteonet.imputation.dnn.gnn.homogeneous.UncertaintyGatNodeImputer method) (pyproteonet.masking.masked_dataset.MaskedDataset method) (pyproteonet.masking.masked_dataset_generator.MaskedDatasetGenerator method)

A

across_sample_aggregate_impute() (in module pyproteonet.imputation.simple) add_positive_gaussian() (in module pyproteonet.simulation.random_error)

add_std_correlated_gaussian() (in module pyproteonet.simulation.random_error) apply() (pyproteonet.data.dataset_sample.DatasetSample method) auto_encoder_impute() (in module pyproteonet.imputation.dnn.autoencoder)

C

calculate_hist() (pyproteonet.data.dataset.Dataset method) calculate_ratio_absolute_error() (in module pyproteonet.metrics.ratios) calculate_sample_pair_ratios() (in module pyproteonet.metrics.ratios) collaborative_filtering_impute() (in module pyproteonet.imputation.dnn.collaborative_filtering) compare_columns() (in module pyproteonet.metrics.abundance_comparison)

compare_columns_molecule_groups() (in module pyproteonet.metrics.abundance_comparison) configure_optimizers() (pyproteonet.imputation.dnn.gnn.heterogeneous.ImputationModule method) copy() (pyproteonet.data.dataset.Dataset method) (pyproteonet.data.dataset_sample.DatasetSample method) create_sample() (pyproteonet.data.dataset.Dataset method)

D

Dataset (class in pyproteonet.data.dataset) dataset (pyproteonet.masking.masked_dataset.MaskedDataset attribute)

DatasetMoleculeValues (class in pyproteonet.data.dataset) DatasetSample (class in pyproteonet.data.dataset_sample) drop_values() (pyproteonet.data.dataset.Dataset method)

E

evaluate_des() (in module pyproteonet.metrics.differential_expression)

F

find_des() (in module pyproteonet.metrics.differential_expression) forward() (pyproteonet.imputation.dnn.gnn.heterogeneous.ImputationModule method) (pyproteonet.imputation.dnn.gnn.homogeneous.UncertaintyGAT method) (pyproteonet.imputation.dnn.gnn.homogeneous.UncertaintyGatNodeImputer method)

from_ids() (pyproteonet.masking.masked_dataset.MaskedDataset class method) from_mapped_dataframe() (pyproteonet.data.dataset.Dataset class method) from_pandas() (pyproteonet.data.dataset.Dataset class method)

G

generic_fancy_impute() (in module pyproteonet.imputation.fancyimpute) generic_matrix_imputation() (in module pyproteonet.imputation.sklearn) get_column_flat() (pyproteonet.data.dataset.Dataset method) get_hidden_ids() (pyproteonet.masking.masked_dataset.MaskedDataset method) get_index_for() (pyproteonet.data.dataset_sample.DatasetSample method) get_lf() (pyproteonet.data.dataset.Dataset method) get_mapped() (pyproteonet.data.dataset.Dataset method) get_mapping_degrees() (pyproteonet.data.molecule_set.MoleculeSet method)

get_mapping_partner() (pyproteonet.data.dataset.Dataset method) (pyproteonet.data.molecule_set.MoleculeSet method) get_mask_ids() (pyproteonet.masking.masked_dataset.MaskedDataset method) get_molecule_subset() (pyproteonet.data.dataset.Dataset method) get_node_values_for_graph() (pyproteonet.data.dataset_sample.DatasetSample method) get_sample() (pyproteonet.masking.masked_dataset.MaskedDataset method) get_samples_value_matrix() (pyproteonet.data.dataset.Dataset method) get_values_flat() (pyproteonet.data.dataset.Dataset method) get_wf() (pyproteonet.data.dataset.Dataset method)

H

has_hidden (pyproteonet.masking.masked_dataset.MaskedDataset property)

hidden (pyproteonet.masking.masked_dataset.MaskedDataset attribute)

I

iBAQ() (in module pyproteonet.aggregation.ibaq) ImputationModule (class in pyproteonet.imputation.dnn.gnn.heterogeneous) impute_heterogeneous_gnn() (in module pyproteonet.imputation.dnn.gnn.heterogeneous) impute_homogeneous_gnn() (in module pyproteonet.imputation.dnn.gnn.homogeneous) impute_local_least_squares() (in module pyproteonet.imputation.r.pca_methods) impute_molecule() (in module pyproteonet.imputation.high_level_api)

impute_ms_core_utils() (in module pyproteonet.imputation.r.ms_core_utils) impute_pca_method() (in module pyproteonet.imputation.r.pca_methods) infer_mapping() (pyproteonet.data.dataset.Dataset method) (pyproteonet.data.molecule_set.MoleculeSet method) iterative_impute() (in module pyproteonet.imputation.sklearn) iterative_svd_impute() (in module pyproteonet.imputation.fancyimpute)

K

keys() (pyproteonet.masking.masked_dataset.MaskedDataset method)

knn_impute() (in module pyproteonet.imputation.sklearn)

L

load() (pyproteonet.data.dataset.Dataset class method) load_crohns_disease_dataset() (in module pyproteonet.io.datasets)

load_example_dataset() (in module pyproteonet.io.datasets) load_maxlfq_benchmark_dataset() (in module pyproteonet.io.datasets) load_maxquant() (in module pyproteonet.io.maxquant)

M

mask_missing() (in module pyproteonet.masking.missing_values) mask_non_missing() (in module pyproteonet.masking.missing_values) masked_dataset_to_homogeneous_graph() (in module pyproteonet.dgl.collate) masked_heterograph_to_homogeneous() (in module pyproteonet.dgl.collate) MaskedDataset (class in pyproteonet.masking.masked_dataset) MaskedDatasetGenerator (class in pyproteonet.masking.masked_dataset_generator) masks (pyproteonet.masking.masked_dataset.MaskedDataset attribute) min_det_impute() (in module pyproteonet.imputation.simple) min_prob_impute() (in module pyproteonet.imputation.r.impute_lcmd) miss_forest_impute() (in module pyproteonet.imputation.r.miss_forest) missing_mask() (pyproteonet.data.dataset_sample.DatasetSample method) missing_molecules() (pyproteonet.data.dataset_sample.DatasetSample method) module pyproteonet.aggregation.ibaq pyproteonet.aggregation.maxlfq pyproteonet.aggregation.partner_aggregation pyproteonet.aggregation.partner_top_n_mean pyproteonet.data.dataset pyproteonet.data.dataset_sample pyproteonet.data.molecule_set pyproteonet.dgl.collate pyproteonet.imputation.dnn.autoencoder pyproteonet.imputation.dnn.collaborative_filtering pyproteonet.imputation.dnn.gnn.heterogeneous pyproteonet.imputation.dnn.gnn.homogeneous pyproteonet.imputation.fancyimpute pyproteonet.imputation.high_level_api pyproteonet.imputation.multistep pyproteonet.imputation.r.impute_lcmd pyproteonet.imputation.r.miss_forest pyproteonet.imputation.r.ms_core_utils pyproteonet.imputation.r.pca_methods pyproteonet.imputation.random_forest pyproteonet.imputation.simple pyproteonet.imputation.sklearn pyproteonet.io.datasets pyproteonet.io.io pyproteonet.io.maxquant pyproteonet.masking.masked_dataset pyproteonet.masking.masked_dataset_generator pyproteonet.masking.missing_values pyproteonet.metrics.abundance_comparison pyproteonet.metrics.differential_expression pyproteonet.metrics.ratios pyproteonet.simulation.protein_peptide pyproteonet.simulation.random_error

MoleculeMapping (class in pyproteonet.data.molecule_set) MoleculeSet (class in pyproteonet.data.molecule_set) multiply_exponential_gaussian() (in module pyproteonet.simulation.random_error) multistep_top3_impute() (in module pyproteonet.imputation.multistep)

N

non_missing_mask() (pyproteonet.data.dataset_sample.DatasetSample method)

non_missing_molecules() (pyproteonet.data.dataset_sample.DatasetSample method) number_molecules() (pyproteonet.data.dataset.Dataset method)

P

plot_hist() (pyproteonet.data.dataset_sample.DatasetSample method) poisson_error() (in module pyproteonet.simulation.random_error) predict_step() (pyproteonet.imputation.dnn.gnn.heterogeneous.ImputationModule method) (pyproteonet.imputation.dnn.gnn.homogeneous.UncertaintyGatNodeImputer method) pyproteonet.aggregation.ibaq module pyproteonet.aggregation.maxlfq module pyproteonet.aggregation.partner_aggregation module pyproteonet.aggregation.partner_top_n_mean module pyproteonet.data.dataset module pyproteonet.data.dataset_sample module pyproteonet.data.molecule_set module pyproteonet.dgl.collate module pyproteonet.imputation.dnn.autoencoder module pyproteonet.imputation.dnn.collaborative_filtering module pyproteonet.imputation.dnn.gnn.heterogeneous module pyproteonet.imputation.dnn.gnn.homogeneous module pyproteonet.imputation.fancyimpute module pyproteonet.imputation.high_level_api module pyproteonet.imputation.multistep module pyproteonet.imputation.r.impute_lcmd module

pyproteonet.imputation.r.miss_forest module pyproteonet.imputation.r.ms_core_utils module pyproteonet.imputation.r.pca_methods module pyproteonet.imputation.random_forest module pyproteonet.imputation.simple module pyproteonet.imputation.sklearn module pyproteonet.io.datasets module pyproteonet.io.io module pyproteonet.io.maxquant module pyproteonet.masking.masked_dataset module pyproteonet.masking.masked_dataset_generator module pyproteonet.masking.missing_values module pyproteonet.metrics.abundance_comparison module pyproteonet.metrics.differential_expression module pyproteonet.metrics.ratios module pyproteonet.simulation.protein_peptide module pyproteonet.simulation.random_error module

R

random_forest_impute() (in module pyproteonet.imputation.random_forest) read_mapped_dataframe() (in module pyproteonet.io.io) read_multiple_mapped_dataframes() (in module pyproteonet.io.io) rename_columns() (pyproteonet.data.dataset.Dataset method)

rename_mapping() (pyproteonet.data.dataset.Dataset method) rename_molecule() (pyproteonet.data.dataset.Dataset method) (pyproteonet.data.molecule_set.MoleculeSet method) rename_values() (pyproteonet.data.dataset.Dataset method)

S

sample_apply() (pyproteonet.data.dataset.Dataset method) save() (pyproteonet.data.dataset.Dataset method) set_column_lf() (pyproteonet.data.dataset.Dataset method) set_hidden() (pyproteonet.masking.masked_dataset.MaskedDataset method) set_hidden_ids() (pyproteonet.masking.masked_dataset.MaskedDataset method)

set_mask() (pyproteonet.masking.masked_dataset.MaskedDataset method) set_mask_ids() (pyproteonet.masking.masked_dataset.MaskedDataset method) set_samples_value_matrix() (pyproteonet.masking.masked_dataset.MaskedDataset method) set_wf() (pyproteonet.data.dataset.Dataset method) simulate_protein_peptide_dataset() (in module pyproteonet.simulation.protein_peptide)

T

to_dgl_graph() (pyproteonet.data.dataset.Dataset method) (pyproteonet.masking.masked_dataset.MaskedDataset method)

training_step() (pyproteonet.imputation.dnn.gnn.heterogeneous.ImputationModule method)

U

UncertaintyGAT (class in pyproteonet.imputation.dnn.gnn.homogeneous)

UncertaintyGatNodeImputer (class in pyproteonet.imputation.dnn.gnn.homogeneous)

V

validation_step() (pyproteonet.imputation.dnn.gnn.heterogeneous.ImputationModule method)

W

write_tsvs() (pyproteonet.data.dataset.Dataset method)