Index

Symbols

--across_run_confidence_threshold pyprophet-infer-glycoform command line option pyprophet-infer-peptidoform command line option --apply_weights pyprophet-score command line option --classifier pyprophet-score command line option --color_palette pyprophet-infer-gene command line option pyprophet-infer-peptide command line option pyprophet-infer-protein command line option --compression pyprophet-export-parquet command line option --compression_level pyprophet-export-parquet command line option --consistent_top pyprophet-export-matrix command line option --context pyprophet-infer-gene command line option pyprophet-infer-glycopeptide command line option pyprophet-infer-peptide command line option pyprophet-infer-protein command line option --csv pyprophet-export-compound command line option pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-tsv command line option --density_estimator pyprophet-infer-glycopeptide command line option --exclude-decoys pyprophet-export-matrix command line option pyprophet-export-tsv command line option --format pyprophet-export-compound command line option pyprophet-export-glyco command line option pyprophet-export-tsv command line option --glycoform pyprophet-export-score-plots command line option --glycoform_match_precursor pyprophet-export-glyco command line option --glycopeptide pyprophet-export-glyco command line option --grid_size pyprophet-infer-glycopeptide command line option --grouped_fdr pyprophet-infer-glycoform command line option --helphelp pyprophet command line option pyprophet-export-compound command line option pyprophet-export-feature-scores command line option pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-parquet command line option pyprophet-export-score-plots command line option pyprophet-export-score-report command line option pyprophet-export-tsv command line option pyprophet-infer-gene command line option pyprophet-infer-glycopeptide command line option pyprophet-infer-peptide command line option pyprophet-infer-protein command line option pyprophet-merge-osw command line option pyprophet-merge-parquet command line option pyprophet-score command line option --in pyprophet-export-compound command line option pyprophet-export-feature-scores command line option pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-parquet command line option pyprophet-export-score-plots command line option pyprophet-export-score-report command line option pyprophet-export-tsv command line option pyprophet-infer-gene command line option pyprophet-infer-glycoform command line option pyprophet-infer-glycopeptide command line option pyprophet-infer-peptide command line option pyprophet-infer-peptidoform command line option pyprophet-infer-protein command line option pyprophet-score command line option --include_transition_data pyprophet-export-parquet command line option --ipf pyprophet-export-matrix command line option pyprophet-export-tsv command line option --ipf_grouped_fdr pyprophet-infer-peptidoform command line option --ipf_h0 pyprophet-infer-peptidoform command line option --ipf_max_alignment_pep pyprophet-infer-peptidoform command line option --ipf_max_peakgroup_pep pyprophet-infer-peptidoform command line option --ipf_max_peptidoform_pep pyprophet-export-matrix command line option pyprophet-export-tsv command line option --ipf_max_precursor_peakgroup_pep pyprophet-infer-peptidoform command line option --ipf_max_precursor_pep pyprophet-infer-peptidoform command line option --ipf_max_transition_pep pyprophet-infer-peptidoform command line option --ipf_ms1_scoring pyprophet-infer-peptidoform command line option --ipf_ms2_scoring pyprophet-infer-peptidoform command line option --level pyprophet-export-matrix command line option pyprophet-score command line option --log-colorize pyprophet command line option --log-level pyprophet command line option --max_alignment_pep pyprophet-export-matrix command line option pyprophet-export-tsv command line option pyprophet-infer-glycoform command line option --max_global_glycopeptide_qvalue pyprophet-export-glyco command line option --max_global_peptide_qvalue pyprophet-export-matrix command line option pyprophet-export-tsv command line option --max_global_protein_qvalue pyprophet-export-matrix command line option pyprophet-export-tsv command line option --max_glycoform_pep pyprophet-export-glyco command line option --max_glycoform_qvalue pyprophet-export-glyco command line option --max_peakgroup_pep pyprophet-infer-glycoform command line option --max_precursor_peakgroup_pep pyprophet-infer-glycoform command line option --max_precursor_pep pyprophet-infer-glycoform command line option --max_rs_peakgroup_qvalue pyprophet-export-compound command line option pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-tsv command line option --max_transition_pep pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-tsv command line option pyprophet-infer-glycoform command line option --merge_transitions pyprophet-merge-parquet command line option --merged_post_scored_runs pyprophet-merge-osw command line option --min_alignment_mapping_confidence pyprophet-infer-peptidoform command line option

--ms1_mz_window pyprophet-infer-glycoform command line option --ms1_mz_window_unit pyprophet-infer-glycoform command line option --ms1_precursor_scoring pyprophet-infer-glycoform command line option --ms2_precursor_scoring pyprophet-infer-glycoform command line option --no-consistent_top pyprophet-export-matrix command line option --no-csv pyprophet-export-compound command line option pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-tsv command line option --no-exclude-decoys pyprophet-export-matrix command line option pyprophet-export-tsv command line option --no-glycoform pyprophet-export-score-plots command line option --no-glycopeptide pyprophet-export-glyco command line option --no-grouped_fdr pyprophet-infer-glycoform command line option --no-include_transition_data pyprophet-export-parquet command line option --no-ipf_grouped_fdr pyprophet-infer-peptidoform command line option --no-ipf_h0 pyprophet-infer-peptidoform command line option --no-ipf_ms1_scoring pyprophet-infer-peptidoform command line option --no-ipf_ms2_scoring pyprophet-infer-peptidoform command line option --no-log-colorize pyprophet command line option --no-merge_transitions pyprophet-merge-parquet command line option --no-ms1_precursor_scoring pyprophet-infer-glycoform command line option --no-ms2_precursor_scoring pyprophet-infer-glycoform command line option --no-parametric pyprophet-infer-gene command line option pyprophet-infer-glycopeptide command line option pyprophet-infer-peptide command line option pyprophet-infer-protein command line option pyprophet-score command line option --no-peptide pyprophet-export-tsv command line option --no-propagate_signal_across_runs pyprophet-infer-glycoform command line option pyprophet-infer-peptidoform command line option --no-protein pyprophet-export-tsv command line option --no-same_run pyprophet-merge-osw command line option --no-split_runs pyprophet-export-parquet command line option --no-split_transition_data pyprophet-export-parquet command line option --no-ss_scale_features pyprophet-score command line option --no-transition_quantification pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-tsv command line option --no-use_alignment pyprophet-export-matrix command line option pyprophet-export-tsv command line option --no-use_alignment_candidates pyprophet-infer-peptidoform command line option --noDecoys pyprophet-export-parquet command line option --normalization pyprophet-export-matrix command line option --onlyFeatures pyprophet-export-parquet command line option --out pyprophet-export-compound command line option pyprophet-export-feature-scores command line option pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-parquet command line option pyprophet-export-tsv command line option pyprophet-infer-gene command line option pyprophet-infer-glycoform command line option pyprophet-infer-glycopeptide command line option pyprophet-infer-peptide command line option pyprophet-infer-peptidoform command line option pyprophet-infer-protein command line option pyprophet-merge-osw command line option pyprophet-merge-parquet command line option pyprophet-score command line option --parametric pyprophet-infer-gene command line option pyprophet-infer-glycopeptide command line option pyprophet-infer-peptide command line option pyprophet-infer-protein command line option pyprophet-score command line option --peptide pyprophet-export-tsv command line option --pqpfile pyprophet-export-parquet command line option --profile pyprophet-score command line option --propagate_signal_across_runs pyprophet-infer-glycoform command line option pyprophet-infer-peptidoform command line option --protein pyprophet-export-tsv command line option --same_run pyprophet-merge-osw command line option --split_runs pyprophet-export-parquet command line option --split_transition_data pyprophet-export-parquet command line option --ss_num_iter pyprophet-score command line option --ss_scale_features pyprophet-score command line option --subsample_ratio pyprophet-score command line option --template pyprophet-merge-osw command line option --threads pyprophet-score command line option --top_n pyprophet-export-matrix command line option --transition_quantification pyprophet-export-glyco command line option pyprophet-export-matrix command line option pyprophet-export-tsv command line option --transitionLevel pyprophet-export-parquet command line option --use_alignment pyprophet-export-matrix command line option pyprophet-export-tsv command line option --use_alignment_candidates pyprophet-infer-peptidoform command line option --use_glycan_composition pyprophet-infer-glycoform command line option --use_glycan_struct pyprophet-infer-glycoform command line option --version pyprophet command line option --xeval_num_iter pyprophet-score command line option

_

__eq__() (pyprophet._base.BaseIOConfig method) (pyprophet._config.ErrorEstimationConfig method) (pyprophet._config.ExportIOConfig method) (pyprophet._config.IPFIOConfig method) (pyprophet._config.LevelContextIOConfig method) (pyprophet._config.RunnerConfig method) (pyprophet._config.RunnerIOConfig method) (pyprophet.io._base.BaseOSWReader method) (pyprophet.io._base.BaseOSWWriter method) (pyprophet.io._base.BaseParquetReader method) (pyprophet.io._base.BaseParquetWriter method) (pyprophet.io._base.BaseReader method) (pyprophet.io._base.BaseSplitParquetReader method) (pyprophet.io._base.BaseSplitParquetWriter method) (pyprophet.io._base.BaseWriter method) __getstate__() (pyprophet.scoring.pyprophet.Scorer method) __hash__ (pyprophet._base.BaseIOConfig attribute) (pyprophet._config.ErrorEstimationConfig attribute) (pyprophet._config.ExportIOConfig attribute) (pyprophet._config.IPFIOConfig attribute) (pyprophet._config.LevelContextIOConfig attribute) (pyprophet._config.RunnerConfig attribute) (pyprophet._config.RunnerIOConfig attribute) (pyprophet.io._base.BaseOSWReader attribute) (pyprophet.io._base.BaseOSWWriter attribute) (pyprophet.io._base.BaseParquetReader attribute) (pyprophet.io._base.BaseParquetWriter attribute) (pyprophet.io._base.BaseReader attribute) (pyprophet.io._base.BaseSplitParquetReader attribute) (pyprophet.io._base.BaseSplitParquetWriter attribute) (pyprophet.io._base.BaseWriter attribute) __init__() (pyprophet._base.BaseIOConfig method) (pyprophet._config.ErrorEstimationConfig method) (pyprophet._config.ExportIOConfig method) (pyprophet._config.IPFIOConfig method) (pyprophet._config.LevelContextIOConfig method) (pyprophet._config.RunnerConfig method) (pyprophet._config.RunnerIOConfig method) (pyprophet.io._base.BaseOSWReader method) (pyprophet.io._base.BaseOSWWriter method) (pyprophet.io._base.BaseParquetReader method) (pyprophet.io._base.BaseParquetWriter method) (pyprophet.io._base.BaseReader method) (pyprophet.io._base.BaseSplitParquetReader method) (pyprophet.io._base.BaseSplitParquetWriter method) (pyprophet.io._base.BaseWriter method) (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.osw.OSWWriter method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.parquet.ParquetWriter method) (pyprophet.io.export.split_parquet.SplitParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetWriter method) (pyprophet.io.ipf.osw.OSWReader method) (pyprophet.io.ipf.osw.OSWWriter method) (pyprophet.io.ipf.parquet.ParquetReader method) (pyprophet.io.ipf.parquet.ParquetWriter method) (pyprophet.io.ipf.split_parquet.SplitParquetReader method) (pyprophet.io.ipf.split_parquet.SplitParquetWriter method) (pyprophet.io.levels_context.osw.OSWReader method) (pyprophet.io.levels_context.osw.OSWWriter method) (pyprophet.io.levels_context.parquet.ParquetReader method) (pyprophet.io.levels_context.parquet.ParquetWriter method) (pyprophet.io.levels_context.split_parquet.SplitParquetReader method) (pyprophet.io.levels_context.split_parquet.SplitParquetWriter method) (pyprophet.io.scoring.osw.OSWReader method) (pyprophet.io.scoring.osw.OSWWriter method) (pyprophet.io.scoring.parquet.ParquetReader method) (pyprophet.io.scoring.parquet.ParquetWriter method) (pyprophet.io.scoring.split_parquet.SplitParquetReader method) (pyprophet.io.scoring.split_parquet.SplitParquetWriter method) (pyprophet.io.scoring.tsv.TSVReader method) (pyprophet.io.scoring.tsv.TSVWriter method) (pyprophet.scoring.classifiers.HistGBCLearner method) (pyprophet.scoring.classifiers.LDALearner method) (pyprophet.scoring.classifiers.SVMLearner method) (pyprophet.scoring.classifiers.XGBLearner method) (pyprophet.scoring.data_handling.Experiment method) (pyprophet.scoring.pyprophet.PyProphet method) (pyprophet.scoring.pyprophet.Scorer method) (pyprophet.scoring.runner.PyProphetRunner method) (pyprophet.scoring.runner.PyProphetWeightApplier method) (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner method) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method) __metaclass__ (pyprophet.scoring.runner.PyProphetRunner attribute) __post_init__() (pyprophet._base.BaseIOConfig method) (pyprophet._config.RunnerIOConfig method) (pyprophet.io._base.BaseWriter method) __repr__() (pyprophet._base.BaseIOConfig method) (pyprophet._config.ErrorEstimationConfig method) (pyprophet._config.ExportIOConfig method) (pyprophet._config.IPFIOConfig method) (pyprophet._config.LevelContextIOConfig method) (pyprophet._config.RunnerConfig method) (pyprophet._config.RunnerIOConfig method) (pyprophet.io._base.BaseOSWReader method) (pyprophet.io._base.BaseOSWWriter method) (pyprophet.io._base.BaseParquetReader method) (pyprophet.io._base.BaseParquetWriter method) (pyprophet.io._base.BaseReader method) (pyprophet.io._base.BaseSplitParquetReader method) (pyprophet.io._base.BaseSplitParquetWriter method) (pyprophet.io._base.BaseWriter method) __setattr__() (pyprophet.scoring.data_handling.Experiment method) __setstate__() (pyprophet.scoring.pyprophet.Scorer method) __str__() (pyprophet._base.BaseIOConfig method) (pyprophet._config.ErrorEstimationConfig method) (pyprophet._config.RunnerConfig method) (pyprophet._config.RunnerIOConfig method) __weakref__ (pyprophet._base.BaseIOConfig attribute) (pyprophet._config.ErrorEstimationConfig attribute) (pyprophet._config.RunnerConfig attribute) (pyprophet.io._base.BaseReader attribute) (pyprophet.io._base.BaseWriter attribute) (pyprophet.io.dispatcher.ReaderDispatcher attribute) (pyprophet.io.dispatcher.WriterDispatcher attribute) (pyprophet.scoring.classifiers.AbstractLearner attribute) (pyprophet.scoring.data_handling.Experiment attribute) (pyprophet.scoring.pyprophet.PyProphet attribute) (pyprophet.scoring.pyprophet.Scorer attribute) (pyprophet.scoring.runner.PyProphetRunner attribute) (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner attribute)

_add_peptide_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _add_protein_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _add_protein_error_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _add_transition_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _apply_weights_on_exp() (pyprophet.scoring.pyprophet.PyProphet method) _augment_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _build_combined_precursor_query() (pyprophet.io.export.osw.OSWWriter method) _build_combined_transition_query() (pyprophet.io.export.osw.OSWWriter method) _build_feature_vars_sql() (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _build_gene_joins() (pyprophet.io.export.osw.OSWWriter method) _build_precursor_query() (pyprophet.io.export.osw.OSWWriter method) _build_result() (pyprophet.scoring.pyprophet.PyProphet method) _build_score_column_selection_and_joins() (pyprophet.io.export.osw.OSWWriter method) _build_score_sql() (pyprophet.io.export.osw.OSWReader method) _build_transition_query() (pyprophet.io.export.osw.OSWWriter method) _build_transition_score_columns_and_join() (pyprophet.io.export.osw.OSWWriter method) _check_alignment_file_exists() (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _check_alignment_presence() (pyprophet.io.export.osw.OSWReader method) _check_contexts() (pyprophet.io.export.osw.OSWWriter method) _check_ipf_presence() (pyprophet.io.export.osw.OSWReader method) _collapse_ipf_peptide_ids() (pyprophet.io._base.BaseParquetReader method) _collapse_protein_ids() (pyprophet.io._base.BaseParquetReader method) _convert_to_single_parquet() (pyprophet.io.export.osw.OSWWriter method) _convert_to_split_parquet() (pyprophet.io.export.osw.OSWWriter method) _create_indexes() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.ipf.osw.OSWReader method) (pyprophet.io.levels_context.osw.OSWReader method) (pyprophet.io.scoring.osw.OSWReader method) _create_temp_table() (pyprophet.io.export.osw.OSWWriter method) _create_unimod_to_codename_peptide_id_mapping_table() (pyprophet.io.export.osw.OSWWriter method) _execute_copy_query() (pyprophet.io._base.BaseWriter method) _export_alignment_data() (pyprophet.io.export.osw.OSWWriter method) _export_combined() (pyprophet.io.export.osw.OSWWriter method) _export_single_file() (pyprophet.io.export.osw.OSWWriter method) _export_split_by_run() (pyprophet.io.export.osw.OSWWriter method) _extra_writes() (pyprophet._config.RunnerIOConfig method) _fetch_alignment_features() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _finalize_feature_table() (pyprophet.io._base.BaseReader method) _get_base_openswath_data() (pyprophet.io.export.osw.OSWReader method) _get_columns_by_prefix() (pyprophet.io._base.BaseSplitParquetReader method) _get_columns_to_keep() (pyprophet.io._base.BaseWriter method) _get_ipf_augmentation_data() (pyprophet.io.export.osw.OSWReader method) _get_ms1_score_info() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _get_parquet_row_count() (pyprophet.io._base.BaseWriter method) _get_peptide_protein_score_table() (pyprophet.io.export.osw.OSWWriter method) _get_peptide_protein_score_table_sqlite() (pyprophet.io.export.osw.OSWReader method) _get_precursor_files() (pyprophet.io.export.split_parquet.SplitParquetReader method) _get_precursor_filter_clause() (pyprophet.io.scoring.osw.OSWReader method) _get_transition_files() (pyprophet.io.export.split_parquet.SplitParquetReader method) _has_im() (pyprophet.io.export.osw.OSWReader method) _has_im_boundaries() (pyprophet.io.export.osw.OSWReader method) _has_peptide_protein_global_scores() (pyprophet.io.export.split_parquet.SplitParquetReader method) _init_duckdb_views() (pyprophet.io._base.BaseOSWReader method), [1] (pyprophet.io._base.BaseSplitParquetReader method) _insert_precursor_peptide_ipf_map() (pyprophet.io.export.osw.OSWWriter method) _is_unscored_file() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _learn() (pyprophet.scoring.pyprophet.PyProphet method) _median_median_normalize() (pyprophet.io._base.BaseWriter method) _median_normalize() (pyprophet.io._base.BaseWriter method) _prepare_column_info() (pyprophet.io.export.osw.OSWWriter method) _prepare_score_dataframe() (pyprophet.io._base.BaseWriter method) _quantile_normalize() (pyprophet.io._base.BaseWriter method) _read_augmented_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _read_for_export_scored_report() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _read_library_data() (pyprophet.io.export.split_parquet.SplitParquetReader method) _read_peptidoform_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _read_sqlite() (pyprophet.io.export.osw.OSWReader method) _read_standard_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _read_unscored_data() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) _read_using_duckdb() (pyprophet.io.scoring.osw.OSWReader method) _read_using_sqlite() (pyprophet.io.scoring.osw.OSWReader method) _register_peptide_ipf_map() (pyprophet.io.export.osw.OSWWriter method) _save_bin_weights() (pyprophet.io._base.BaseWriter method) _save_tsv_weights() (pyprophet.io._base.BaseWriter method) _setup_experiment() (pyprophet.scoring.pyprophet.PyProphet method) _summarize_gene_level() (pyprophet.io._base.BaseWriter method) _summarize_peptide_level() (pyprophet.io._base.BaseWriter method) _summarize_precursor_level() (pyprophet.io._base.BaseWriter method) _summarize_protein_level() (pyprophet.io._base.BaseWriter method) _validate_row_count_after_join() (pyprophet.io._base.BaseWriter method) _write_levels_context_pdf_report() (pyprophet.io._base.BaseWriter method) _write_parquet() (pyprophet.io.export.osw.OSWWriter method) _write_pdf_report() (pyprophet.io._base.BaseWriter method)

A

AbstractLearner (class in pyprophet.scoring.classifiers) AbstractSemiSupervisedLearner (class in pyprophet.scoring.semi_supervised) across_run_confidence_threshold (pyprophet._config.IPFIOConfig attribute) add_alignment_features (pyprophet._config.RunnerConfig attribute) add_chromatogram_probabilities() (pyprophet.scoring.pyprophet.Scorer method) add_peak_group_rank() (pyprophet.scoring.data_handling.Experiment method)

apply_bm (class in pyprophet.ipf) apply_weights() (pyprophet.scoring.pyprophet.PyProphet method) autotune (pyprophet._config.RunnerConfig attribute) averaged_learner() (pyprophet.scoring.classifiers.AbstractLearner class method) (pyprophet.scoring.classifiers.LinearLearner class method) (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner method) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method)

B

BaseIOConfig (class in pyprophet._base) BaseOSWReader (class in pyprophet.io._base) BaseOSWWriter (class in pyprophet.io._base) BaseParquetReader (class in pyprophet.io._base)

BaseParquetWriter (class in pyprophet.io._base) BaseReader (class in pyprophet.io._base) BaseSplitParquetReader (class in pyprophet.io._base) BaseSplitParquetWriter (class in pyprophet.io._base) BaseWriter (class in pyprophet.io._base)

C

check_for_unique_blocks (class in pyprophet.scoring.data_handling) classifier (pyprophet._config.RunnerConfig attribute) (pyprophet.io._base.BaseOSWReader attribute) (pyprophet.io._base.BaseOSWWriter attribute) (pyprophet.io._base.BaseParquetReader attribute) (pyprophet.io._base.BaseParquetWriter attribute) (pyprophet.io._base.BaseSplitParquetReader attribute) (pyprophet.io._base.BaseSplitParquetWriter attribute) (pyprophet.io.ipf.osw.OSWReader attribute) (pyprophet.io.ipf.osw.OSWWriter attribute) (pyprophet.io.ipf.parquet.ParquetReader attribute) (pyprophet.io.ipf.parquet.ParquetWriter attribute) (pyprophet.io.ipf.split_parquet.SplitParquetReader attribute) (pyprophet.io.ipf.split_parquet.SplitParquetWriter attribute) (pyprophet.io.levels_context.osw.OSWReader attribute) (pyprophet.io.levels_context.osw.OSWWriter attribute) (pyprophet.io.levels_context.parquet.ParquetReader attribute) (pyprophet.io.levels_context.parquet.ParquetWriter attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetReader attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.osw.OSWReader attribute) (pyprophet.io.scoring.osw.OSWWriter attribute) (pyprophet.io.scoring.parquet.ParquetReader attribute) (pyprophet.io.scoring.parquet.ParquetWriter attribute) (pyprophet.io.scoring.split_parquet.SplitParquetReader attribute) (pyprophet.io.scoring.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.tsv.TSVReader attribute) (pyprophet.io.scoring.tsv.TSVWriter attribute) (pyprophet.scoring.pyprophet.Scorer attribute)

clean_and_export_library() (pyprophet.io._base.BaseWriter method) cleanup_and_check (class in pyprophet.scoring.data_handling) color_palette (pyprophet._config.LevelContextIOConfig attribute) (pyprophet._config.RunnerConfig attribute) compression_level (pyprophet._config.ExportIOConfig attribute) compression_method (pyprophet._config.ExportIOConfig attribute) compute_model_fdr (class in pyprophet.ipf) config (pyprophet.scoring.pyprophet.PyProphet attribute) (pyprophet.scoring.runner.PyProphetRunner attribute) consistent_top (pyprophet._config.ExportIOConfig attribute) context (pyprophet._base.BaseIOConfig attribute) (pyprophet._config.RunnerIOConfig attribute) context_fdr (pyprophet._config.LevelContextIOConfig attribute) copy() (pyprophet._base.BaseIOConfig method)

D

density_estimator (pyprophet._config.LevelContextIOConfig attribute) (pyprophet._config.RunnerConfig attribute)

df (pyprophet.scoring.data_handling.Experiment attribute)

E

error_estimation_config (pyprophet._config.LevelContextIOConfig attribute) (pyprophet._config.RunnerConfig attribute) error_stat (pyprophet.scoring.pyprophet.Scorer attribute) ErrorEstimationConfig (class in pyprophet._config) Experiment (class in pyprophet.scoring.data_handling) export() (pyprophet.io.export.osw.OSWWriter method) export_feature_scores() (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method)

export_format (pyprophet._config.ExportIOConfig attribute) export_quant_matrix() (pyprophet.io._base.BaseWriter method) export_results() (pyprophet.io._base.BaseWriter method) ExportIOConfig (class in pyprophet._config) extra_writes (pyprophet._config.RunnerIOConfig attribute)

F

file_type (pyprophet._base.BaseIOConfig attribute) filter_() (pyprophet.scoring.data_handling.Experiment method) from_cli_args() (pyprophet._config.IPFIOConfig class method) (pyprophet._config.LevelContextIOConfig class method) (pyprophet._config.RunnerIOConfig class method)

from_config() (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner class method)

G

get_decoy_peaks() (pyprophet.scoring.data_handling.Experiment method) get_delta_td_bt_feature_size() (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method) get_error_stats() (pyprophet.scoring.pyprophet.Scorer method) get_feature_matrix() (pyprophet.scoring.data_handling.Experiment method) get_parameters() (pyprophet.scoring.classifiers.AbstractLearner method) (pyprophet.scoring.classifiers.HistGBCLearner method) (pyprophet.scoring.classifiers.LDALearner method) (pyprophet.scoring.classifiers.SVMLearner method) (pyprophet.scoring.classifiers.XGBLearner method) get_reader() (pyprophet.io.dispatcher.ReaderDispatcher static method) get_target_peaks() (pyprophet.scoring.data_handling.Experiment method) get_top_decoy_peaks() (pyprophet.scoring.data_handling.Experiment method) get_top_target_peaks() (pyprophet.scoring.data_handling.Experiment method) get_top_test_peaks() (pyprophet.scoring.data_handling.Experiment method) get_train_peaks() (pyprophet.scoring.data_handling.Experiment method) get_weights() (pyprophet.scoring.classifiers.LinearLearner method) get_writer() (pyprophet.io.dispatcher.WriterDispatcher static method) glyco (pyprophet._config.RunnerConfig attribute) (pyprophet.io._base.BaseOSWReader attribute) (pyprophet.io._base.BaseOSWWriter attribute) (pyprophet.io._base.BaseParquetReader attribute) (pyprophet.io._base.BaseParquetWriter attribute) (pyprophet.io._base.BaseSplitParquetReader attribute) (pyprophet.io._base.BaseSplitParquetWriter attribute) (pyprophet.io.ipf.osw.OSWReader attribute) (pyprophet.io.ipf.osw.OSWWriter attribute) (pyprophet.io.ipf.parquet.ParquetReader attribute) (pyprophet.io.ipf.parquet.ParquetWriter attribute) (pyprophet.io.ipf.split_parquet.SplitParquetReader attribute) (pyprophet.io.ipf.split_parquet.SplitParquetWriter attribute) (pyprophet.io.levels_context.osw.OSWReader attribute) (pyprophet.io.levels_context.osw.OSWWriter attribute) (pyprophet.io.levels_context.parquet.ParquetReader attribute) (pyprophet.io.levels_context.parquet.ParquetWriter attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetReader attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.osw.OSWReader attribute) (pyprophet.io.scoring.osw.OSWWriter attribute) (pyprophet.io.scoring.parquet.ParquetReader attribute) (pyprophet.io.scoring.parquet.ParquetWriter attribute) (pyprophet.io.scoring.split_parquet.SplitParquetReader attribute) (pyprophet.io.scoring.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.tsv.TSVReader attribute) (pyprophet.io.scoring.tsv.TSVWriter attribute)

grid_size (pyprophet._config.LevelContextIOConfig attribute) (pyprophet._config.RunnerConfig attribute) group_id (pyprophet._config.RunnerConfig attribute)

H

HistGBCLearner (class in pyprophet.scoring.classifiers)

I

im_calibration (pyprophet._config.ExportIOConfig attribute) infer_genes (class in pyprophet.levels_contexts) infer_glycopeptides (class in pyprophet.levels_contexts) infer_peptides (class in pyprophet.levels_contexts) infer_peptidoforms (class in pyprophet.ipf) infer_proteins (class in pyprophet.levels_contexts) infile (pyprophet._base.BaseIOConfig attribute) (pyprophet._config.RunnerIOConfig attribute) (pyprophet.io._base.BaseOSWReader attribute) (pyprophet.io._base.BaseOSWWriter attribute) (pyprophet.io._base.BaseParquetReader attribute) (pyprophet.io._base.BaseParquetWriter attribute) (pyprophet.io._base.BaseSplitParquetReader attribute) (pyprophet.io._base.BaseSplitParquetWriter attribute) (pyprophet.io.ipf.osw.OSWReader attribute) (pyprophet.io.ipf.osw.OSWWriter attribute) (pyprophet.io.ipf.parquet.ParquetReader attribute) (pyprophet.io.ipf.parquet.ParquetWriter attribute) (pyprophet.io.ipf.split_parquet.SplitParquetReader attribute) (pyprophet.io.ipf.split_parquet.SplitParquetWriter attribute) (pyprophet.io.levels_context.osw.OSWReader attribute) (pyprophet.io.levels_context.osw.OSWWriter attribute) (pyprophet.io.levels_context.parquet.ParquetReader attribute) (pyprophet.io.levels_context.parquet.ParquetWriter attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetReader attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.osw.OSWReader attribute) (pyprophet.io.scoring.osw.OSWWriter attribute) (pyprophet.io.scoring.parquet.ParquetReader attribute) (pyprophet.io.scoring.parquet.ParquetWriter attribute) (pyprophet.io.scoring.split_parquet.SplitParquetReader attribute) (pyprophet.io.scoring.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.tsv.TSVReader attribute) (pyprophet.io.scoring.tsv.TSVWriter attribute)

INFILES pyprophet-merge-osw command line option pyprophet-merge-parquet command line option inner_learner (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) intensity_calibration (pyprophet._config.ExportIOConfig attribute) ipf (pyprophet._config.ExportIOConfig attribute) ipf_grouped_fdr (pyprophet._config.IPFIOConfig attribute) ipf_h0 (pyprophet._config.IPFIOConfig attribute) ipf_max_alignment_pep (pyprophet._config.IPFIOConfig attribute) ipf_max_peakgroup_pep (pyprophet._config.IPFIOConfig attribute) (pyprophet._config.RunnerConfig attribute) ipf_max_peakgroup_rank (pyprophet._config.RunnerConfig attribute) ipf_max_peptidoform_pep (pyprophet._config.ExportIOConfig attribute) ipf_max_precursor_peakgroup_pep (pyprophet._config.IPFIOConfig attribute) ipf_max_precursor_pep (pyprophet._config.IPFIOConfig attribute) ipf_max_transition_isotope_overlap (pyprophet._config.RunnerConfig attribute) ipf_max_transition_pep (pyprophet._config.IPFIOConfig attribute) ipf_min_transition_sn (pyprophet._config.RunnerConfig attribute) ipf_ms1_scoring (pyprophet._config.IPFIOConfig attribute) ipf_ms2_scoring (pyprophet._config.IPFIOConfig attribute) IPFIOConfig (class in pyprophet._config) iter_semi_supervised_learning() (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner method) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method)

K

keep_decoys (pyprophet._config.ExportIOConfig attribute)

L

LDALearner (class in pyprophet.scoring.classifiers) learn() (pyprophet.scoring.classifiers.AbstractLearner method) (pyprophet.scoring.classifiers.HistGBCLearner method) (pyprophet.scoring.classifiers.LDALearner method) (pyprophet.scoring.classifiers.SVMLearner method) (pyprophet.scoring.classifiers.XGBLearner method) learn_and_apply() (pyprophet.scoring.pyprophet.PyProphet method) learn_final() (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner method) learn_randomized() (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner method) level (pyprophet._base.BaseIOConfig attribute) (pyprophet._config.RunnerIOConfig attribute) (pyprophet.io._base.BaseOSWReader attribute) (pyprophet.io._base.BaseOSWWriter attribute) (pyprophet.io._base.BaseParquetReader attribute) (pyprophet.io._base.BaseParquetWriter attribute) (pyprophet.io._base.BaseSplitParquetReader attribute) (pyprophet.io._base.BaseSplitParquetWriter attribute) (pyprophet.io.ipf.osw.OSWReader attribute) (pyprophet.io.ipf.osw.OSWWriter attribute) (pyprophet.io.ipf.parquet.ParquetReader attribute) (pyprophet.io.ipf.parquet.ParquetWriter attribute) (pyprophet.io.ipf.split_parquet.SplitParquetReader attribute) (pyprophet.io.ipf.split_parquet.SplitParquetWriter attribute) (pyprophet.io.levels_context.osw.OSWReader attribute) (pyprophet.io.levels_context.osw.OSWWriter attribute) (pyprophet.io.levels_context.parquet.ParquetReader attribute) (pyprophet.io.levels_context.parquet.ParquetWriter attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetReader attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.osw.OSWReader attribute) (pyprophet.io.scoring.osw.OSWWriter attribute) (pyprophet.io.scoring.parquet.ParquetReader attribute) (pyprophet.io.scoring.parquet.ParquetWriter attribute) (pyprophet.io.scoring.split_parquet.SplitParquetReader attribute) (pyprophet.io.scoring.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.tsv.TSVReader attribute) (pyprophet.io.scoring.tsv.TSVWriter attribute) (pyprophet.scoring.pyprophet.Scorer attribute)

LevelContextIOConfig (class in pyprophet._config) lfdr_adj (pyprophet._config.ErrorEstimationConfig attribute) lfdr_eps (pyprophet._config.ErrorEstimationConfig attribute) lfdr_monotone (pyprophet._config.ErrorEstimationConfig attribute) lfdr_transformation (pyprophet._config.ErrorEstimationConfig attribute) lfdr_truncate (pyprophet._config.ErrorEstimationConfig attribute) LinearLearner (class in pyprophet.scoring.classifiers) log_summary() (pyprophet.scoring.data_handling.Experiment method)

M

main_score_selection_report (pyprophet._config.RunnerConfig attribute) max_alignment_pep (pyprophet._config.ExportIOConfig attribute) max_global_peptide_qvalue (pyprophet._config.ExportIOConfig attribute) max_global_protein_qvalue (pyprophet._config.ExportIOConfig attribute) max_rs_peakgroup_qvalue (pyprophet._config.ExportIOConfig attribute) max_transition_pep (pyprophet._config.ExportIOConfig attribute) merge_files() (pyprophet.io._base.BaseSplitParquetWriter method) min_alignment_mapping_confidence (pyprophet._config.IPFIOConfig attribute) min_fragments (pyprophet._config.ExportIOConfig attribute) minimal_error_stat() (pyprophet.scoring.pyprophet.Scorer method) module pyprophet._base pyprophet._config pyprophet.cli pyprophet.io pyprophet.io.export pyprophet.io.ipf pyprophet.io.levels_context pyprophet.io.scoring pyprophet.ipf pyprophet.levels_contexts pyprophet.scoring

N

normalization (pyprophet._config.ExportIOConfig attribute)

normalize_score_by_decoys() (pyprophet.scoring.data_handling.Experiment method)

O

OSWReader (class in pyprophet.io.export.osw) (class in pyprophet.io.ipf.osw) (class in pyprophet.io.levels_context.osw) (class in pyprophet.io.scoring.osw) OSWWriter (class in pyprophet.io.export.osw) (class in pyprophet.io.ipf.osw) (class in pyprophet.io.levels_context.osw) (class in pyprophet.io.scoring.osw) out_type (pyprophet._config.ExportIOConfig attribute) outfile (pyprophet._base.BaseIOConfig attribute) (pyprophet._config.RunnerIOConfig attribute) (pyprophet.io._base.BaseOSWReader attribute) (pyprophet.io._base.BaseOSWWriter attribute) (pyprophet.io._base.BaseParquetReader attribute) (pyprophet.io._base.BaseParquetWriter attribute) (pyprophet.io._base.BaseSplitParquetReader attribute) (pyprophet.io._base.BaseSplitParquetWriter attribute) (pyprophet.io.ipf.osw.OSWReader attribute) (pyprophet.io.ipf.osw.OSWWriter attribute) (pyprophet.io.ipf.parquet.ParquetReader attribute) (pyprophet.io.ipf.parquet.ParquetWriter attribute) (pyprophet.io.ipf.split_parquet.SplitParquetReader attribute) (pyprophet.io.ipf.split_parquet.SplitParquetWriter attribute) (pyprophet.io.levels_context.osw.OSWReader attribute) (pyprophet.io.levels_context.osw.OSWWriter attribute) (pyprophet.io.levels_context.parquet.ParquetReader attribute) (pyprophet.io.levels_context.parquet.ParquetWriter attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetReader attribute) (pyprophet.io.levels_context.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.osw.OSWReader attribute) (pyprophet.io.scoring.osw.OSWWriter attribute) (pyprophet.io.scoring.parquet.ParquetReader attribute) (pyprophet.io.scoring.parquet.ParquetWriter attribute) (pyprophet.io.scoring.split_parquet.SplitParquetReader attribute) (pyprophet.io.scoring.split_parquet.SplitParquetWriter attribute) (pyprophet.io.scoring.tsv.TSVReader attribute) (pyprophet.io.scoring.tsv.TSVWriter attribute)

P

parametric (pyprophet._config.ErrorEstimationConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) ParquetReader (class in pyprophet.io.export.parquet) (class in pyprophet.io.ipf.parquet) (class in pyprophet.io.levels_context.parquet) (class in pyprophet.io.scoring.parquet) ParquetWriter (class in pyprophet.io.export.parquet) (class in pyprophet.io.ipf.parquet) (class in pyprophet.io.levels_context.parquet) (class in pyprophet.io.scoring.parquet) peptide (pyprophet._config.ExportIOConfig attribute) peptidoform_inference (class in pyprophet.ipf) pfdr (pyprophet._config.ErrorEstimationConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) pi0 (pyprophet.scoring.pyprophet.Scorer attribute) pi0_lambda (pyprophet._config.ErrorEstimationConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) pi0_method (pyprophet._config.ErrorEstimationConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) pi0_smooth_df (pyprophet._config.ErrorEstimationConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) pi0_smooth_log_pi0 (pyprophet._config.ErrorEstimationConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) pqp_file (pyprophet._config.ExportIOConfig attribute) precursor_inference (class in pyprophet.ipf) prefix (pyprophet._base.BaseIOConfig attribute) (pyprophet._config.RunnerIOConfig attribute) prepare_data_table (class in pyprophet.scoring.data_handling) prepare_precursor_bm (class in pyprophet.ipf) prepare_transition_bm (class in pyprophet.ipf) propagate_signal_across_runs (pyprophet._config.IPFIOConfig attribute) protein (pyprophet._config.ExportIOConfig attribute) PyProphet (class in pyprophet.scoring.pyprophet) pyprophet command line option --helphelp --log-colorize --log-level --no-log-colorize --version pyprophet-export-compound command line option --csv --format --helphelp --in --max_rs_peakgroup_qvalue --no-csv --out pyprophet-export-feature-scores command line option --helphelp --in --out pyprophet-export-glyco command line option --csv --format --glycoform_match_precursor --glycopeptide --helphelp --in --max_global_glycopeptide_qvalue --max_glycoform_pep --max_glycoform_qvalue --max_rs_peakgroup_qvalue --max_transition_pep --no-csv --no-glycopeptide --no-transition_quantification --out --transition_quantification pyprophet-export-matrix command line option --consistent_top --csv --exclude-decoys --helphelp --in --ipf --ipf_max_peptidoform_pep --level --max_alignment_pep --max_global_peptide_qvalue --max_global_protein_qvalue --max_rs_peakgroup_qvalue --max_transition_pep --no-consistent_top --no-csv --no-exclude-decoys --no-transition_quantification --no-use_alignment --normalization --out --top_n --transition_quantification --use_alignment pyprophet-export-parquet command line option --compression --compression_level --helphelp --in --include_transition_data --no-include_transition_data --no-split_runs --no-split_transition_data --noDecoys --onlyFeatures --out --pqpfile --split_runs --split_transition_data --transitionLevel pyprophet-export-score-plots command line option --glycoform --helphelp --in --no-glycoform pyprophet-export-score-report command line option --helphelp --in pyprophet-export-tsv command line option --csv --exclude-decoys --format --helphelp --in --ipf --ipf_max_peptidoform_pep --max_alignment_pep --max_global_peptide_qvalue --max_global_protein_qvalue --max_rs_peakgroup_qvalue --max_transition_pep --no-csv --no-exclude-decoys --no-peptide --no-protein --no-transition_quantification --no-use_alignment --out --peptide --protein --transition_quantification --use_alignment

pyprophet-infer-gene command line option --color_palette --context --helphelp --in --no-parametric --out --parametric pyprophet-infer-glycoform command line option --across_run_confidence_threshold --grouped_fdr --in --max_alignment_pep --max_peakgroup_pep --max_precursor_peakgroup_pep --max_precursor_pep --max_transition_pep --ms1_mz_window --ms1_mz_window_unit --ms1_precursor_scoring --ms2_precursor_scoring --no-grouped_fdr --no-ms1_precursor_scoring --no-ms2_precursor_scoring --no-propagate_signal_across_runs --out --propagate_signal_across_runs --use_glycan_composition --use_glycan_struct pyprophet-infer-glycopeptide command line option --context --density_estimator --grid_size --helphelp --in --no-parametric --out --parametric pyprophet-infer-peptide command line option --color_palette --context --helphelp --in --no-parametric --out --parametric pyprophet-infer-peptidoform command line option --across_run_confidence_threshold --in --ipf_grouped_fdr --ipf_h0 --ipf_max_alignment_pep --ipf_max_peakgroup_pep --ipf_max_precursor_peakgroup_pep --ipf_max_precursor_pep --ipf_max_transition_pep --ipf_ms1_scoring --ipf_ms2_scoring --min_alignment_mapping_confidence --no-ipf_grouped_fdr --no-ipf_h0 --no-ipf_ms1_scoring --no-ipf_ms2_scoring --no-propagate_signal_across_runs --no-use_alignment_candidates --out --propagate_signal_across_runs --use_alignment_candidates pyprophet-infer-protein command line option --color_palette --context --helphelp --in --no-parametric --out --parametric pyprophet-merge-osw command line option --helphelp --merged_post_scored_runs --no-same_run --out --same_run --template INFILES pyprophet-merge-parquet command line option --helphelp --merge_transitions --no-merge_transitions --out INFILES pyprophet-score command line option --apply_weights --classifier --helphelp --in --level --no-parametric --no-ss_scale_features --out --parametric --profile --ss_num_iter --ss_scale_features --subsample_ratio --threads --xeval_num_iter pyprophet._base module pyprophet._config module pyprophet.cli module pyprophet.io module pyprophet.io.export module pyprophet.io.ipf module pyprophet.io.levels_context module pyprophet.io.scoring module pyprophet.ipf module pyprophet.levels_contexts module pyprophet.scoring module PyProphetLearner (class in pyprophet.scoring.runner) PyProphetRunner (class in pyprophet.scoring.runner) PyProphetWeightApplier (class in pyprophet.scoring.runner)

R

rank_by() (pyprophet.scoring.data_handling.Experiment method) read() (pyprophet.io._base.BaseOSWReader method), [1] (pyprophet.io._base.BaseParquetReader method), [1] (pyprophet.io._base.BaseReader method) (pyprophet.io._base.BaseSplitParquetReader method), [1] (pyprophet.io.export.osw.OSWReader method) (pyprophet.io.export.parquet.ParquetReader method) (pyprophet.io.export.split_parquet.SplitParquetReader method) (pyprophet.io.ipf.osw.OSWReader method), [1] (pyprophet.io.ipf.parquet.ParquetReader method), [1] (pyprophet.io.ipf.split_parquet.SplitParquetReader method), [1] (pyprophet.io.levels_context.osw.OSWReader method), [1] (pyprophet.io.levels_context.parquet.ParquetReader method), [1] (pyprophet.io.levels_context.split_parquet.SplitParquetReader method), [1] (pyprophet.io.scoring.osw.OSWReader method), [1] (pyprophet.io.scoring.parquet.ParquetReader method), [1] (pyprophet.io.scoring.split_parquet.SplitParquetReader method), [1] (pyprophet.io.scoring.tsv.TSVReader method), [1]

reader (pyprophet.scoring.runner.PyProphetRunner attribute) ReaderDispatcher (class in pyprophet.io.dispatcher) rt_calibration (pyprophet._config.ExportIOConfig attribute) rt_unit (pyprophet._config.ExportIOConfig attribute) run() (pyprophet.scoring.runner.PyProphetRunner method) run_algo() (pyprophet.scoring.runner.PyProphetLearner method) (pyprophet.scoring.runner.PyProphetRunner method) (pyprophet.scoring.runner.PyProphetWeightApplier method) runner (pyprophet._config.RunnerIOConfig attribute) RunnerConfig (class in pyprophet._config) RunnerIOConfig (class in pyprophet._config)

S

save_results() (pyprophet.io._base.BaseOSWWriter method), [1] (pyprophet.io._base.BaseParquetWriter method), [1] (pyprophet.io._base.BaseSplitParquetWriter method), [1] (pyprophet.io._base.BaseWriter method) (pyprophet.io.ipf.osw.OSWWriter method), [1] (pyprophet.io.ipf.parquet.ParquetWriter method), [1] (pyprophet.io.ipf.split_parquet.SplitParquetWriter method), [1] (pyprophet.io.levels_context.osw.OSWWriter method), [1] (pyprophet.io.levels_context.parquet.ParquetWriter method), [1] (pyprophet.io.levels_context.split_parquet.SplitParquetWriter method), [1] (pyprophet.io.scoring.osw.OSWWriter method), [1] (pyprophet.io.scoring.parquet.ParquetWriter method), [1] (pyprophet.io.scoring.split_parquet.SplitParquetWriter method), [1] (pyprophet.io.scoring.tsv.TSVWriter method), [1] save_weights() (pyprophet.io._base.BaseOSWWriter method) (pyprophet.io._base.BaseParquetWriter method) (pyprophet.io._base.BaseSplitParquetWriter method) (pyprophet.io._base.BaseWriter method) (pyprophet.io.ipf.osw.OSWWriter method) (pyprophet.io.ipf.parquet.ParquetWriter method) (pyprophet.io.ipf.split_parquet.SplitParquetWriter method) (pyprophet.io.levels_context.osw.OSWWriter method) (pyprophet.io.levels_context.parquet.ParquetWriter method) (pyprophet.io.levels_context.split_parquet.SplitParquetWriter method) (pyprophet.io.scoring.osw.OSWWriter method), [1] (pyprophet.io.scoring.parquet.ParquetWriter method) (pyprophet.io.scoring.split_parquet.SplitParquetWriter method) (pyprophet.io.scoring.tsv.TSVWriter method) scale_features() (pyprophet.scoring.data_handling.Experiment method) score() (pyprophet.scoring.classifiers.AbstractLearner method) (pyprophet.scoring.classifiers.HistGBCLearner method) (pyprophet.scoring.classifiers.LinearLearner method) (pyprophet.scoring.classifiers.SVMLearner method) (pyprophet.scoring.classifiers.XGBLearner method) (pyprophet.scoring.pyprophet.Scorer method) (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner method) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method) score_columns (pyprophet.scoring.pyprophet.Scorer attribute)

Scorer (class in pyprophet.scoring.pyprophet) select_train_peaks() (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method) semi_supervised_learner (pyprophet.scoring.pyprophet.PyProphet attribute) set_and_rerank() (pyprophet.scoring.data_handling.Experiment method) set_learner() (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method) set_parameters() (pyprophet.scoring.classifiers.AbstractLearner method) (pyprophet.scoring.classifiers.HistGBCLearner method) (pyprophet.scoring.classifiers.LDALearner method) (pyprophet.scoring.classifiers.LinearLearner method) (pyprophet.scoring.classifiers.SVMLearner method) (pyprophet.scoring.classifiers.XGBLearner method) split_for_xval() (pyprophet.scoring.data_handling.Experiment method) split_runs (pyprophet._config.ExportIOConfig attribute) split_transition_data (pyprophet._config.ExportIOConfig attribute) SplitParquetReader (class in pyprophet.io.export.split_parquet) (class in pyprophet.io.ipf.split_parquet) (class in pyprophet.io.levels_context.split_parquet) (class in pyprophet.io.scoring.split_parquet) SplitParquetWriter (class in pyprophet.io.export.split_parquet) (class in pyprophet.io.ipf.split_parquet) (class in pyprophet.io.levels_context.split_parquet) (class in pyprophet.io.scoring.split_parquet) ss_initial_fdr (pyprophet._config.RunnerConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) ss_iteration_fdr (pyprophet._config.RunnerConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) ss_main_score (pyprophet._config.RunnerConfig attribute) ss_num_iter (pyprophet._config.RunnerConfig attribute) ss_scale_features (pyprophet._config.RunnerConfig attribute) ss_score_filter (pyprophet._config.RunnerConfig attribute) ss_use_dynamic_main_score (pyprophet._config.RunnerConfig attribute) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner attribute) StandardSemiSupervisedLearner (class in pyprophet.scoring.semi_supervised) start_semi_supervised_learning() (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner method) (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method) statistics_report (class in pyprophet.levels_contexts) subsample_ratio (pyprophet._base.BaseIOConfig attribute) SVMLearner (class in pyprophet.scoring.classifiers)

T

table (pyprophet.scoring.runner.PyProphetRunner attribute) test (pyprophet._config.ExportIOConfig attribute) (pyprophet._config.RunnerConfig attribute) (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner attribute) threads (pyprophet._config.RunnerConfig attribute) top_n (pyprophet._config.ExportIOConfig attribute) transfer_confident_evidence_across_runs (class in pyprophet.ipf)

transition_quantification (pyprophet._config.ExportIOConfig attribute) tric_chromprob (pyprophet._config.RunnerConfig attribute) TSVReader (class in pyprophet.io.scoring.tsv) TSVWriter (class in pyprophet.io.scoring.tsv) tune() (pyprophet.scoring.classifiers.HistGBCLearner method) (pyprophet.scoring.classifiers.SVMLearner method) (pyprophet.scoring.classifiers.XGBLearner method) tune_semi_supervised_learning() (pyprophet.scoring.semi_supervised.StandardSemiSupervisedLearner method)

U

update_chosen_main_score_in_table (class in pyprophet.scoring.data_handling) use_alignment (pyprophet._config.ExportIOConfig attribute)

use_alignment_candidates (pyprophet._config.IPFIOConfig attribute) use_metabolomics_scores (class in pyprophet.scoring.data_handling)

W

writer (pyprophet.scoring.runner.PyProphetRunner attribute)

WriterDispatcher (class in pyprophet.io.dispatcher)

X

xeval_fraction (pyprophet._config.RunnerConfig attribute) (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner attribute) xeval_num_iter (pyprophet._config.RunnerConfig attribute) (pyprophet.scoring.semi_supervised.AbstractSemiSupervisedLearner attribute)

xgb_params (pyprophet._config.RunnerConfig attribute) XGBLearner (class in pyprophet.scoring.classifiers)