API reference

Tools for working with raw data

tidyms.Assay([assay_path, data_path, ...])	Manages data preprocessing workflows from raw data to data matrix.
tidyms.MSData([ms_mode, instrument, ...])	Reader object for raw MS data.
tidyms.Chromatogram(time, spint[, index, mode])	Representation of a chromatogram.
tidyms.MSSpectrum(mz, spint[, time, ...])	Representation of a Mass Spectrum.

Tools for working with processed data

tidyms.DataContainer(data_matrix, ...[, ...])	Container object that stores processed metabolomics data.
tidyms.filter.Pipeline(processors[, verbose])	Combines Filters and Correctors and applies them simultaneously.

List of available filters and processors

tidyms.filter.BatchCorrector([min_qc_dr, ...])	Correct time dependant systematic bias along samples due to variation in instrumental response.
tidyms.filter.BlankCorrector([...])	Corrects systematic bias due to sample preparation.
tidyms.filter.ClassRemover(classes)	Remove samples from the specified classes.
tidyms.filter.DilutionFilter([min_corr, ...])	Filter features based on the correlation with a dilution factor.
tidyms.filter.DRatioFilter([lb, ub, robust, ...])	Remove Features with low biological information.
tidyms.filter.PrevalenceFilter([...])	Remove Features detected in a low number of samples.
tidyms.filter.VariationFilter([lb, ub, ...])	Remove features with low reproducibility.

Tools for working with chemical data

tidyms.chem.Formula(*args)	Represents a chemical formula as a mapping from isotopes to formula coefficients.
tidyms.chem.PeriodicTable()	Reference the PeriodicTable object.
tidyms.chem.FormulaGenerator(bounds[, max_M])	Generates sum formulas based on exact mass values.
tidyms.chem.EnvelopeScorer(bounds[, max_M, ...])	Ranks formula candidates by comparing a measured isotopic envelope against the theoretical envelopes of candidates.

Module reference

tidyms.container	Objects used to store and manage metabolomics data
tidyms.correspondence	Functions used to match features
tidyms.fileio	Functions and objects to work with mzML data and tabular data obtained from third party software used to process Mass Spectrometry data.
tidyms.filter	Tools to filter and correct DataContainers.
tidyms.lcms	Functions and objects for working with LC-MS data.
tidyms.peaks	functions and objects used to detect peaks.
tidyms.raw_data_utils	Functions used to extract information from raw data.
tidyms.utils	Utility functions used inside several modules.
tidyms.chem.atoms	Tools for working with Isotopes and Elements.
tidyms.chem.envelope_tools	Scores sum formula candidates using the isotopic envelope.
tidyms.chem.formula	Tools for working with chemical formulas
tidyms.dartms	Functionality to process DART-MS datasets