Index

_

__author__ (in module PhenoFeatureFinder)

__version__ (in module PhenoFeatureFinder)

B

baseline_performance (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute), [1], [2] best_ensemble_models_searched (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute), [1] best_model (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute)

bioassay (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis attribute) bioassay_csv (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis attribute) blank_features_filtered (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute), [1]

C

calculate_percentile() (in module PhenoFeatureFinder.utils) combine_seperately_counted_versions_of_last_recorded_stage() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method) compute_metabolome_sparsity() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method), [1] compute_metrics_classification() (in module PhenoFeatureFinder.utils) compute_pca_on_metabolites() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method)

convert_counts_to_cumulative() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method) correct_cumulative_counts() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method) create_density_plot() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method) create_df_with_max_counts_per_stage() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method) create_sample_score_plot() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method) create_scree_plot() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method)

D

discard_features_detected_in_blanks() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method), [1]

E

exp_variance (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute)

extract_samples_to_condition() (in module PhenoFeatureFinder.utils)

F

feature_loadings (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute) FeatureSelection (class in PhenoFeatureFinder.feature_selection_using_ml)

filter_features_per_group_by_percentile() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method), [1] filter_out_unreliable_features() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method), [1] filtered_by_percentile_value (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute), [1]

G

get_baseline_performance() (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection method), [1]

get_names_of_top_n_features_from_selected_pc() (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection method)

I

impute_missing_values_with_median() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method), [1]

M

median_of_ratios_normalisation() (in module PhenoFeatureFinder.utils) metabolome (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute), [1] (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute), [1] metabolome_pca_reduced (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute) metabolome_validated (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute), [1] (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute), [1] (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis attribute)

module PhenoFeatureFinder PhenoFeatureFinder.feature_selection_using_ml PhenoFeatureFinder.omics_analysis PhenoFeatureFinder.phenotype_analysis PhenoFeatureFinder.utils

O

OmicsAnalysis (class in PhenoFeatureFinder.omics_analysis)

P

pc_importances (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute) pca_performed (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute), [1] PhenoFeatureFinder module PhenoFeatureFinder.feature_selection_using_ml module PhenoFeatureFinder.omics_analysis module PhenoFeatureFinder.phenotype_analysis module

PhenoFeatureFinder.utils module phenotype (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute), [1] phenotype_validated (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection attribute), [1] PhenotypeAnalysis (class in PhenoFeatureFinder.phenotype_analysis) plot_confusion_matrix() (in module PhenoFeatureFinder.utils) plot_counts_per_stage() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method) plot_development_over_time_in_fitted_model() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method) plot_features_in_upset_plot() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method) plot_survival_over_time_in_fitted_model() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method) prepare_for_plotting() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method)

R

reshape_to_wide() (PhenoFeatureFinder.phenotype_analysis.PhenotypeAnalysis method)

S

search_best_model_with_tpot_and_compute_pc_importances() (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection method)

search_best_model_with_tpot_and_get_feature_importances() (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection method) sparsity (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute), [1]

T

tpot_custom_config (in module PhenoFeatureFinder.feature_selection_using_ml)

U

unreliable_features_filtered (PhenoFeatureFinder.omics_analysis.OmicsAnalysis attribute), [1]

V

validate_input_metabolome_df() (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection method), [1] (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method), [1]

validate_input_phenotype_df() (PhenoFeatureFinder.feature_selection_using_ml.FeatureSelection method), [1]

W

write_clean_metabolome_to_csv() (PhenoFeatureFinder.omics_analysis.OmicsAnalysis method), [1]