emzed.quantification.chromatogram_integration module¶
- emzed.quantification.chromatogram_integration.create_result_table(chromatogram_table, peak_shape_model, post_fixes, result, path, overwrite, in_place)[source]¶
- emzed.quantification.chromatogram_integration.integrate_chromatograms(chromatogram_table, peak_shape_model, ms_level=None, show_progress=True, n_cores=1, min_size_for_parallel_execution=100, post_fixes=None, max_cores=8, in_place=False, path=None, overwrite=False, **model_extra_args)[source]¶
integrates peaks of chromatogram_table.
- Parameters:
chromatogram_table –
emzed.Table
with required columnsid, mzmin, mzmax, rtmin, rtmax, peakmap
.peak_shape_model – String of model name applied to determine peak area. Available models are:
asym_gauss
,linear
,no_integration
,sgolay
,emg
.ms_level – MS level of peak integration. Must only be specified if peakmap has more than one MS levels.
Default = None
.show_progress – Boolean value to activate progress bar.
Default = 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
.min_size_for_parallel_execution – Defines the number of table rows required to execute multicore processing.
Default = 100
.post_fixes – Defines a subset of peaks via postfixes i. e. [‘__0’, ‘__1’]. By default, all peak_tables of a table get integrated.
Default = 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 then_cores
is set tomax_cores
. Default is8
.in_place – Allows operation in place if True. Note: if
in_place
isTrue
multicore processing is not possible and n_cores is set to 1. Default =False
. Using in-place integration has performance benefits.path – If specified the result will be a Table with a db file backend, else the result will be managed in memory.
overwrite – Indicate if an already existing database file should be overwritten.
- Returns:
emzed.Table
by default. Returns None ifin_place
isTrue