Index

A

accumulate_spectra() (in module tidyms.raw_data_utils) add_data_processing_step() (DartMSAssay method) add_order_from_csv() (DataContainer method), [1] annotate_features() (DartMSAssay method)

annotate_isotopologues() (Assay method) annotate_with_compounds() (DartMSAssay method) Annotation (class in tidyms.lcms) array1d_to_str() (in module tidyms.utils) Assay (class in tidyms)

B

batch (DataContainer property), [1] batch correction batch_correction() (DartMSAssay method) BatchCorrector (class in tidyms.filter), [1] BatchInformationError blank correction

blank_subtraction() (DartMSAssay method) BlankCorrector (class in tidyms.filter), [1] BokehPlotMethods (class in tidyms.container) bracket_consensus_spectrum_samples() (DartMSAssay method) build_data_matrix() (DartMSAssay method) build_feature_table() (Assay method)

C

calc_2D_Embedding() (DartMSAssay method) calc_volcano_plots() (DartMSAssay method) calculate_consensus_spectra_for_samples() (DartMSAssay method) carryover Chromatogram (class in tidyms) (class in tidyms.lcms) classes (DataContainer property), [1] ClassNameError ClassRemover (class in tidyms.filter), [1] clone_DartMSAssay() (DartMSAssay method) cluster_quality_check_function__peak_form() (in module tidyms.dartms)

cluster_quality_check_function__ppmDeviationCheck() (in module tidyms.dartms) cohen_d() (in module tidyms.dartms) compute_isotopic_envelope() (Peak static method) correct_batches() (PreprocessMethods method) correct_MZ_shift_across_samples() (DartMSAssay method) correction correlation() (MetricMethods method) correlation_histogram() (SeabornPlotMethods method) create_assay_from_chronogramFiles() (DartMSAssay static method) cv() (in module tidyms.utils) (MetricMethods method)

D

DartMSAssay (class in tidyms.dartms) data curation data matrix DataContainer (class in tidyms) (class in tidyms.container) describe() (Peak method) describe_features() (Assay method) detect_features() (Assay method) detect_peaks() (in module tidyms.peaks) detection_rate() (in module tidyms.utils) (MetricMethods method)

diagnose() (DataContainer method), [1] DilutionFilter (class in tidyms.filter), [1] DilutionInformationError download_dataset() (in module tidyms.fileio) download_tidyms_data() (in module tidyms.fileio) dratio() (MetricMethods method) DRatioFilter (class in tidyms.filter), [1] drop_lower_spectra() (DartMSAssay method) DuplicateMerger (class in tidyms.filter)

E

Element (class in tidyms.chem.atoms) EmptyDataContainerError EnvelopeScorer (class in tidyms.chem) (class in tidyms.chem.envelope_tools) EnvelopeValidator (class in tidyms.chem.envelope_tools)

estimate_baseline() (in module tidyms.peaks) estimate_noise() (in module tidyms.peaks) export_data_matrix() (DartMSAssay method) export_for_R() (DartMSAssay method) extract_features() (Assay method) (LCTrace method)

F

feature Feature (class in tidyms.lcms) feature correspondence feature descriptor feature detection feature table feature() (BokehPlotMethods method) fill_missing() (Assay method) fill_nan() (MZTrace method) filtration

find_centroids() (in module tidyms.peaks) (MSSpectrum method), [1] find_closest() (in module tidyms.utils) Formula (class in tidyms.chem) (class in tidyms.chem.formula) FormulaGenerator (class in tidyms.chem) from_hmdb() (FormulaGenerator static method) from_pickle() (DataContainer static method), [1] from_progenesis() (DataContainer static method), [1] from_string() (Roi class method)

G

gauss() (in module tidyms.utils) gaussian_mixture() (in module tidyms.utils) generate_database_template() (DartMSAssay static method) generate_feature_abundance_plot() (DartMSAssay method) generate_feature_raw_plot() (DartMSAssay method) generate_formulas() (FormulaGenerator method) get_abundances() (Element method) get_area() (Peak method) get_chromatogram() (MSData method), [1] (MSData_from_file method) (MSData_in_memory method) (MSData_Proxy method) (MSData_simulated method) (MSData_subset_spectra method) get_data_matrix_and_meta() (DartMSAssay method) get_exact_mass() (Formula method), [1] get_extension() (Peak method) get_filename() (in module tidyms.utils) get_find_centroid_params() (in module tidyms.lcms) get_height() (Peak method) get_isotopic_envelope() (Formula method), [1] get_mmi() (Element method) get_monoisotope() (Element method) get_ms_data() (Assay method) get_mz() (Peak method) get_mz_std() (Peak method) get_n_chromatograms() (MSData method), [1] (MSData_from_file method) (MSData_in_memory method) (MSData_Proxy method) (MSData_simulated method) (MSData_subset_spectra method)

get_n_spectra() (MSData method), [1] (MSData_from_file method) (MSData_in_memory method) (MSData_Proxy method) (MSData_simulated method) (MSData_subset_spectra method) get_nominal_mass() (Formula method), [1] get_rt() (Peak method) get_rt_end() (Peak method) get_rt_start() (Peak method) get_sample_metadata() (Assay method) get_settings() (in module tidyms.utils) get_snr() (Peak method) get_spectra_iterator() (MSData method), [1] (MSData_from_file method) (MSData_in_memory method) (MSData_Proxy method) (MSData_simulated method) (MSData_subset_spectra method) get_spectrum() (MSData method), [1] (MSData_from_file method) (MSData_in_memory method) (MSData_Proxy method) (MSData_simulated method) (MSData_subset_spectra method) get_summary_of_results() (DartMSAssay method) get_tidyms_path() (in module tidyms.utils) get_top_results() (EnvelopeScorer method), [1] get_width() (Peak method)

I

id (DataContainer property), [1] import_filter_artifact_removal() (in module tidyms.dartms) import_filter_mz_range() (in module tidyms.dartms) import_filter_remove_signals_below_intensity() (in module tidyms.dartms) InvalidFormula

InvalidIsotope InvalidPeakException is_notebook() (in module tidyms.utils) is_valid_class_name() (DataContainer method), [1] Isotope (class in tidyms.chem.atoms)

L

LCTrace (class in tidyms.lcms) list_available_datasets() (in module tidyms.fileio) load_dataset() (in module tidyms.fileio)

load_features() (Assay method) load_roi() (Assay method) load_roi_list() (Assay method)

M

mad() (in module tidyms.utils) make_chromatograms() (in module tidyms.raw_data_utils) make_data_matrix() (Assay method) make_formula_coefficients_envelopes() (in module tidyms.chem.envelope_tools) make_roi() (in module tidyms.raw_data_utils) make_tic() (in module tidyms.raw_data_utils) mapping match_features() (Assay method) (in module tidyms.correspondence) metadata_correlation() (in module tidyms.utils) MetricMethods (class in tidyms.container) MissingMappingInformation MissingValueError module tidyms.chem.atoms tidyms.chem.envelope_tools tidyms.chem.formula tidyms.container tidyms.correspondence tidyms.dartms tidyms.fileio tidyms.filter tidyms.lcms tidyms.peaks tidyms.raw_data_utils tidyms.utils

MSData (class in tidyms) (class in tidyms.fileio) MSData_from_file (class in tidyms.fileio) MSData_in_memory (class in tidyms.fileio) MSData_Proxy (class in tidyms.fileio) MSData_simulated (class in tidyms.fileio) MSData_subset_spectra (class in tidyms.fileio) MSSpectrum (class in tidyms) (class in tidyms.lcms) MZTrace (class in tidyms.lcms)

N

normalization normalize() (in module tidyms.utils) (PreprocessMethods method)

normalize_samples_by_TIC() (DartMSAssay method) normalize_to_internal_standard() (DartMSAssay method)

O

order (DataContainer property), [1]

P

pca() (MetricMethods method) pca_loadings() (BokehPlotMethods method) (SeabornPlotMethods method) pca_scores() (BokehPlotMethods method) (SeabornPlotMethods method) Peak (class in tidyms.lcms) PeriodicTable() (in module tidyms.chem) (in module tidyms.chem.atoms) Pipeline (class in tidyms.filter), [1] plot() (LCTrace method) (MSSpectrum method), [1] plot_feature_mz_deviations() (DartMSAssay method)

plot_heatmap() (DartMSAssay method) plot_mz_deviation_overview() (DartMSAssay method) plot_RSDs_per_group() (DartMSAssay method) plot_sample_abundances() (DartMSAssay method) plot_sample_TICs() (DartMSAssay method) prefab_DARTMS_dataProcessing_pipeline() (in module tidyms.dartms) PreprocessMethods (class in tidyms.container) prevalence filter PrevalenceFilter (class in tidyms.filter), [1] print_results_overview() (DartMSAssay method) print_sample_overview() (DartMSAssay method) Processor (class in tidyms.filter)

Q

quality control sample

R

read_data_matrix() (in module tidyms.fileio) read_from_dill_file() (DartMSAssay static method) read_mzmine() (in module tidyms.fileio) read_pickle() (in module tidyms.fileio) read_progenesis() (in module tidyms.fileio) read_xcms() (in module tidyms.fileio) register() (in module tidyms.filter) remove() (DataContainer method), [1] Reporter (class in tidyms.filter)

reset() (DataContainer method), [1] restrict_to_high_quality_features__found_in_replicates() (DartMSAssay method) restrict_to_high_quality_features__low_RSD_in_groups() (DartMSAssay method) restrict_to_high_quality_features__minimum_intensity_filter() (DartMSAssay method) restrict_to_high_quality_features__most_n_abundant() (DartMSAssay method) results_to_array() (FormulaGenerator method) robust_cv() (in module tidyms.utils) Roi (class in tidyms.lcms) run order RunOrderError

S

sample class sample descriptor sample type sample_to_path() (in module tidyms.utils) save() (DataContainer method), [1] save_self_to_dill_file() (DartMSAssay method) scale() (in module tidyms.utils) (PreprocessMethods method) scaling score() (EnvelopeScorer method), [1] score_envelope() (in module tidyms.chem.envelope_tools) sd_ratio() (in module tidyms.utils)

SeabornPlotMethods (class in tidyms.container) select_features() (DataContainer method), [1] select_top_n_spectra() (DartMSAssay method) set_data() (DartMSAssay method) set_default_order() (DataContainer method), [1] set_plot_mode() (DataContainer method), [1] show_sample_overview() (DartMSAssay static method) sort() (DataContainer method), [1] str_to_array1d() (in module tidyms.utils) subset_features() (DartMSAssay method) subset_samples() (DartMSAssay method) system suitability check

T

tidyms.chem.atoms module tidyms.chem.envelope_tools module tidyms.chem.formula module tidyms.container module tidyms.correspondence module tidyms.dartms module tidyms.fileio module

tidyms.filter module tidyms.lcms module tidyms.peaks module tidyms.raw_data_utils module tidyms.utils module to_csv() (DataContainer method), [1] to_string() (MZTrace method) (Roi method) transform() (in module tidyms.utils) (PreprocessMethods method)

V

VariationFilter (class in tidyms.filter), [1]

W

write_bracketing_results_to_featureML() (DartMSAssay method)

write_consensus_spectrum_to_featureML_file_per_sample() (DartMSAssay method)