dimspy package

Subpackages

• dimspy.models package
  • Submodules
  • dimspy.models.peak_matrix module
  • dimspy.models.peaklist module
  • dimspy.models.peaklist_metadata module
  • dimspy.models.peaklist_tags module
  • Module contents
• dimspy.portals package
  • Submodules
  • dimspy.portals.hdf5_portal module
  • dimspy.portals.mzml_portal module
  • dimspy.portals.paths module
  • dimspy.portals.thermo_raw_portal module
  • dimspy.portals.txt_portal module
  • Module contents
• dimspy.process package
  • Submodules
  • dimspy.process.mass_calibration module
  • dimspy.process.peak_alignment module
  • dimspy.process.peak_filters module
  • dimspy.process.scan_processing module
  • Module contents

Submodules

dimspy.dimspy module

dimspy.dimspy.main()

dimspy.experiment module

dimspy.experiment.mz_range_from_header(h)

dimspy.experiment.ms_type_from_header(h)

dimspy.experiment.scan_type_from_header(h)

dimspy.experiment.mode_type_from_header(h)

dimspy.experiment.count_scan_types(hs)

dimspy.experiment.count_ms_types(hs)

dimspy.experiment.interpret_experiment(mzrs)

dimspy.experiment.check_metadata(fn_tsv)

dimspy.experiment.update_metadata(peaklists, fl)

dimspy.experiment.idxs_reps_from_filelist(replicates)

dimspy.experiment.update_class_labels(pm, fn_tsv)

dimspy.log_setting module

log_setting: provide functions to config logging system.

author(s): Albert origin: Dec. 11, 2014

class dimspy.log_setting.LevelFormatter(fmt_dict=None, *args, **kwargs)

Bases: logging.Formatter

format(record)

dimspy.log_setting.set_logging(level=20, print_formatter=None, log_file=None, log_mode='w', log_formatter=None, exception_format=None)

dimspy.workflow module

dimspy.workflow.process_scans(source, function_noise, snr_thres, ppm, min_fraction=None, rsd_thres=None, min_scans=1, filelist=None, skip_stitching=False, remove_mz_range=None, ringing_thres=None, filter_scan_events=None, block_size=2000, ncpus=None)

dimspy.workflow.stitch(source, function_noise, snr_thres, ppm, min_fraction=None, rsd_thres=None, min_scans=1, filelist=None, skip_stitching=False, remove_mz_range=None, ringing_thres=None, filter_scan_events=None, block_size=2000, ncpus=None)

dimspy.workflow.replicate_filter(source, ppm, replicates, min_peaks, rsd_thres=None, filelist=None, block_size=2000, ncpus=None)

dimspy.workflow.align_samples(source, ppm, filelist=None, block_size=2000, ncpus=None)

dimspy.workflow.blank_filter(peak_matrix, blank_label, min_fraction=1.0, min_fold_change=1.0, function='mean', rm_samples=True, class_labels=None)

dimspy.workflow.sample_filter(peak_matrix, min_fraction, within=False, rsd=None, qc_label=None, class_labels=None)

dimspy.workflow.hdf5_to_txt(fname, path_out, attr_name='intensity', separator='\t', transpose=False, comprehensive=False)

dimspy.workflow.merge_peaklists(source, filelist=None)

dimspy.workflow.load_peaklists(source)

Module contents