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workflows

workflows

Overview

This module provides premade data processing workflows for untargeted metabolomics analysis. The workflows include feature detection, alignment, annotation, normalization, and statistical analysis. The module also includes functions for batch file processing and evaluating the data quality of raw files.

Functions

process_single_file

process_single_file(file_name, params=None, segment_feature=True, group_features=False, evaluate_peak_shape=True, annotate_ms2=False, ms2_library_path=None, output_dir=None)

Performs untargeted feature detection for a single file.

Parameters:

  • file_name (str): Path to the raw file.
  • params (Params object, optional): Parameters for feature detection. If None, the default parameters are used based on the type of mass spectrometer.
  • segment_feature (bool, default True): Whether to segment the feature to peaks for distinguishing possible isomers.
  • group_features (bool, default False): Whether to group features by isotopes, adducts, and in-source fragments.
  • evaluate_peak_shape (bool, default True): Whether to evaluate the peak shape by calculating noise score and asymmetry factor.
  • annotate_ms2 (bool, default False): Whether to annotate MS2 spectra.
  • ms2_library_path (str, optional): Path to the MS2 library.
  • output_dir (str, optional): The output directory for the single file. If None, the output is saved to the same directory as the raw file.

Returns:

  • d (MSData object): An MSData object containing the processed data.

Usage:

# use default parameters for processing a single file
result = feature_detection("sample.mzML")

untargeted_metabolomics_workflow

untargeted_metabolomics_workflow(path=None, return_results=False, only_process_single_files=False, return_params_only=False)

The untargeted metabolomics workflow.

Parameters:

  • path (str, optional): The working directory. If None, the current working directory is used.
  • return_results (bool, default False): Whether to return the results.
  • only_process_single_files (bool, default False): Whether to only process the single files.
  • return_params_only (bool, default False): Whether to return the parameters only.

Returns:

  • features (list): A list of features.
  • params (Params object): Parameters for the workflow.

Usage:

untargeted_metabolomics_workflow(path="/path/to/project")

batch_file_processing

batch_file_processing(path=None, segment_feature=True, group_features=False, evaluate_peak_shape=True, annotate_ms2=True, ms2_library_path=None, cpu_ratio=0.8, batch_size=100)

Process single files using default parameters. This function is useful for batch processing of multiple files. Files from different ion modes are allowed, but parameters cannot be specified for individual files, and default parameters are used.

Parameters:

  • path (str, optional): The working directory. If None, the current working directory is used.
  • segment_feature (bool, default True): Whether to segment the feature to peaks for distinguishing possible isomers.
  • group_features (bool, default False): Whether to group features by isotopes, adducts, and in-source fragments.
  • evaluate_peak_shape (bool, default True): Whether to evaluate the peak shape by calculating noise score and asymmetry factor.
  • annotate_ms2 (bool, default True): Whether to annotate MS2 spectra.
  • ms2_library_path (str, optional): The path to the MS2 library.
  • cpu_ratio (float, default 0.8): The percentage of CPU cores to use.
  • batch_size (int, default 100): The number of files to process in each batch.

run_evaluation

run_evaluation(path=None, zscore_threshold=-2)

Evaluate the run and report the problematic files. The path to the project directory should be organized as follows:

path
├── single_files
│   ├── sample1.txt
│   ├── sample2.txt
│   └── ...
└── ...

where single_files contains the processed files in txt format.

Parameters:

  • path (str, optional): Path to the project directory.
  • zscore_threshold (float, default -2): The threshold of z-score for detecting problematic files.
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