params

Overview

The params module defines a class Params to store and manage parameters for mass spectrometry data processing. The class provides methods to read parameters from a CSV file, set default parameters based on the type of mass spectrometer and ionization mode, check the validity of parameters, and output parameters to a file. The module also includes a function find_ms_info to determine the type of mass spectrometer and ionization mode from a raw file.

Classes

`Params`

A class to store and manage parameters for mass spectrometry data processing.

Attributes:

sample_names (list): Sample names without extension.
sample_abs_paths (list): Absolute paths of the raw MS data.
sample_metadata (DataFrame): Sample metadata.
project_dir (str): Project directory.
sample_dir (str): Directory for the raw MS data.
single_file_dir (str): Directory for the single file output.
tmp_file_dir (str): Directory for the intermediate file output.
ms2_matching_dir (str): Directory for the MS2 matching output.
bpc_dir (str): Directory for the base peak chromatogram output.
project_file_dir (str): Directory for the project files.
normalization_dir (str): Directory for the normalization output.
statistics_dir (str): Directory for the statistical analysis output.
problematic_files (dict): Problematic files.
file_name (str): File name of the raw data.
file_path (str): Absolute path of the raw data.
ion_mode (str): MS ion mode.
ms_type (str): Type of MS.
is_centroid (bool): Whether the raw data is centroid data.
file_format (str): File type in lower case.
time (datetime): When the data file was acquired.
scan_time_unit (str): Time unit of the scan time.
mz_lower_limit (float): Lower limit of m/z in Da.
mz_upper_limit (float): Upper limit of m/z in Da.
rt_lower_limit (float): Lower limit of RT in minutes.
rt_upper_limit (float): Upper limit of RT in minutes.
scan_levels (list): Scan levels to be read.
centroid_mz_tol (float): m/z tolerance for centroiding.
ms1_abs_int_tol (float): Absolute intensity threshold for MS1.
ms2_abs_int_tol (float): Absolute intensity threshold for MS2.
ms2_rel_int_tol (float): Relative intensity threshold to base peak for MS2.
precursor_mz_offset (float): Offset for MS2 m/z range in Da.
mz_tol_ms1 (float): m/z tolerance for MS1.
mz_tol_ms2 (float): m/z tolerance for MS2.
feature_gap_tol (int): Gap tolerance within a feature.
batch_size (int): Batch size for parallel processing.
percent_cpu_to_use (float): Percentage of CPU to use.
group_features_single_file (bool): Whether to group features in a single file.
scan_scan_cor_tol (float): Scan-to-scan correlation tolerance for feature grouping.
mz_tol_feature_grouping (float): m/z tolerance for feature grouping.
rt_tol_feature_grouping (float): RT tolerance for feature grouping.
valid_charge_states (list): Valid charge states for feature grouping.
mz_tol_alignment (float): m/z tolerance for alignment.
rt_tol_alignment (float): RT tolerance for alignment.
correct_rt (bool): Whether to perform RT correction.
scan_number_cutoff (int): Feature with non-zero scan number greater than the cutoff will be aligned.
detection_rate_cutoff (float): Features detected need to be >rate*(qc+sample).
merge_features (bool): Whether to merge features with almost the same m/z and RT.
mz_tol_merge_features (float): m/z tolerance for merging features.
rt_tol_merge_features (float): RT tolerance for merging features.
group_features_after_alignment (bool): Whether to group features after alignment.
fill_gaps (bool): Whether to fill the gaps in the aligned features.
gap_filling_method (str): Method for gap filling.
gap_filling_rt_window (float): RT window for finding local maximum.
ms2_library_path (str): Path to the MS2 library.
ms2_sim_tol (float): MS2 similarity tolerance.
fuzzy_search (bool): Whether to perform fuzzy search.
sample_normalization (bool): Whether to normalize the data based on total sample amount/concentration.
sample_norm_method (str): Sample normalization method.
signal_normalization (bool): Whether to run feature-wised normalization to correct systematic signal drift.
signal_norm_method (str): Normalization method for signal drift.
run_statistics (bool): Whether to perform statistical analysis.
plot_bpc (bool): Whether to plot base peak chromatograms.
plot_ms2 (bool): Whether to plot mirror plots for MS2 matching.
plot_normalization (bool): Whether to plot the normalization results.
by_group_name (str): Group name for classifier building.
output_single_file (bool): Whether to output the processed individual files to a csv file.
output_ms1_scans (bool): Whether to output all MS1 scans to a pickle file for faster data reloading.
output_aligned_file (bool): Whether to output aligned features to a csv file.
quant_method (str): Value for quantification and output.

Methods:

read_parameters_from_csv(path): Read parameters from a CSV file.
read_sample_metadata(path): Read sample metadata from a CSV file.
_untargeted_metabolomics_workflow_preparation(): Prepare the parameters for the untargeted metabolomics workflow.
set_default(ms_type, ion_mode): Set the parameters by the type of MS.
check_parameters(): Check if the parameters are correct using PARAMETER_RAGES.
output_parameters(path, format="json"): Output the parameters to a file.

Functions

find_ms_info

find_ms_info(file_name)

Find the type of mass spectrometer and ionization mode from the raw file.

Parameters:

file_name (str): The file name of the raw file.

Returns:

ms_type (str): The type of MS, “orbitrap”, “qtof”, “tripletof” or “others”.
ion_mode (str): The ion mode, “positive” or “negative”.
centroid (bool): Whether the data is centroid data.

Constants

valid parameter ranges

PARAMETER_RAGES

A dictionary of valid parameter ranges.

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PARAMETER_RAGES = {
    "mz_lower_limit": (0.0, 100000.0),
    "mz_upper_limit": (0.0, 100000.0),
    "rt_lower_limit": (0.0, 10000.0),
    "rt_upper_limit": (0.0, 10000.0),
    "centroid_mz_tol": (0.0, 0.1),
    "ms1_abs_int_tol": (0, 1e10),
    "ms2_abs_int_tol": (0, 1e10),
    "ms2_rel_int_tol": (0.0, 1.0),
    "precursor_mz_offset": (0.0, 100000.0),
    "mz_tol_ms1": (0.0, 0.02),
    "mz_tol_ms2": (0.0, 0.02),
    "feature_gap_tol": (0, 100),
    "scan_scan_cor_tol": (0.0, 1.0),
    "mz_tol_alignment": (0.0, 0.02),
    "rt_tol_alignment": (0.0, 2.0),
    "scan_number_cutoff": (0, 100),
    "detection_rate_cutoff": (0.0, 1.0),
    "mz_tol_merge_features": (0.0, 0.02),
    "rt_tol_merge_features": (0.0, 0.5),
    "ms2_sim_tol": (0.0, 1.0)
}

default parameters

PARAMETER_DEFAULT

A dictionary of default parameters.

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PARAMETER_DEFAULT = {
    "mz_lower_limit": 0.0,
    "mz_upper_limit": 100000.0,
    "rt_lower_limit": 0.0,
    "rt_upper_limit": 10000.0,
    "centroid_mz_tol": 0.005,
    "ms1_abs_int_tol": 1000.0,
    "ms2_abs_int_tol": 500,
    "ms2_rel_int_tol": 0.01,
    "precursor_mz_offset": 2.0,
    "mz_tol_ms1": 0.01,
    "mz_tol_ms2": 0.015,
    "feature_gap_tol": 30,
    "scan_scan_cor_tol": 0.7,
    "mz_tol_alignment": 0.01,
    "rt_tol_alignment": 0.2,
    "scan_number_cutoff": 5,
    "detection_rate_cutoff": 0.1,
    "mz_tol_merge_features": 0.01,
    "rt_tol_merge_features": 0.05,
    "ms2_sim_tol": 0.7
}

normalization raw_data_utils