Skip to content

emzed.quantification

integrate(peak_table, peak_shape_model, ms_level=None, show_progress=True, n_cores=1, min_size_for_parallel_execution=MIN_SIZE_DEFAULT, post_fixes=None, max_cores=8, in_place=False, path=None, overwrite=False, **model_extra_args)

integrates peaks of peak_table.

Parameters:

Name Type Description Default
peak_table

emzed.Table with required columns id, mzmin, mzmax, rtmin, rtmax, peakmap.

 required
peak_shape_model

String of model name applied to determine peak area. Available models are: asym_gauss, linear, no_integration, sgolay, emg.

 required
ms_level

MS level of peak integration. Must only be specified if peakmap has more than one MS levels. Default = None.

 None
show_progress

Boolean value to activate progress bar. Default = True.

 True
n_cores

Defines the number of cores used for multicore processing. If n_cores exceeds the number of available cores a warning is displayed and. Default = 1. On Windows, prefer available_cores - 1 (at least 1) for interactive work.

 1
min_size_for_parallel_execution

Defines the number of table rows required to execute multicore processing. Default = 100.

 MIN_SIZE_DEFAULT
post_fixes

Defines a subset of peaks via postfixes i. e. ['__0', '__1']. By default, all peaks in a table row are integrated. Default = None.

 None
max_cores

The maximal number of cores used for multicore processing. If max_cores exceeds the number of available cores a warning is displayed and the n_cores is set to max_cores. Default is 8.

 8
in_place

Allows operation in place if True. Note: if in_place is True multicore processing is not possible and n_cores is set to 1. Default = False. Using in-place integration has performance benefits.

 False
path

If specified the result will be a Table with a db file backend, else the result will be managed in memory.

 None
overwrite

Indicate if an already existing database file should be overwritten.

 False

Returns:

Type Description

emzed.Table by default. Returns None if in_place is True

Example:

t1 = emzed.quantification.integrate(t, "linear")

The result keeps the original peak columns and adds: peak_shape_model, area, rmse, and valid_model.

integrate_chromatograms(chromatogram_table, peak_shape_model, ms_level=None, show_progress=True, n_cores=1, min_size_for_parallel_execution=MIN_SIZE_DEFAULT, post_fixes=None, max_cores=8, in_place=False, path=None, overwrite=False, **model_extra_args)

integrates peaks of chromatogram_table.

Parameters:

Name Type Description Default
chromatogram_table

emzed.Table with required columns id, mzmin, mzmax, rtmin, rtmax, peakmap.

 required
peak_shape_model

String of model name applied to determine peak area. Available models are: asym_gauss, linear, no_integration, sgolay, emg.

 required
ms_level

MS level of peak integration. Must only be specified if peakmap has more than one MS levels. Default = None.

 None
show_progress

Boolean value to activate progress bar. Default = True.

 True
n_cores

Defines the number of cores used for multicore processing. If n_cores exceeds the number of available cores a warning is displayed and. Default = 1. On Windows, prefer available_cores - 1 (at least 1) for interactive work.

 1
min_size_for_parallel_execution

Defines the number of table rows required to execute multicore processing. Default = 100.

 MIN_SIZE_DEFAULT
post_fixes

Defines a subset of peaks via postfixes i. e. ['__0', '__1']. By default, all peaks in a table row are integrated. Default = None.

 None
max_cores

The maximal number of cores used for multicore processing. If max_cores exceeds the number of available cores a warning is displayed and the n_cores is set to max_cores. Default is 8.

 8
in_place

Allows operation in place if True. Note: if in_place is True multicore processing is not possible and n_cores is set to 1. Default = False. Using in-place integration has performance benefits.

 False
path

If specified the result will be a Table with a db file backend, else the result will be managed in memory.

 None
overwrite

Indicate if an already existing database file should be overwritten.

 False

Returns:

Type Description

emzed.Table by default. Returns None if in_place is True