emzed.peak_picking¶
extract_chromatograms(peak_table, ms_level=None, post_fixes=None, path=None, overwrite=False)
¶
Extract chromatograms from table with peak map and peak limits.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
peak_table
|
Table with columns rtmin*, rtmax*, mzmin*, mzmax* and peakmap* for given post_fixes. |
required | |
ms_level
|
optional MS level to consider. |
None
|
|
post_fixes
|
optional post_fixes to consider. |
None
|
|
path
|
optional path for out-of-memory table. |
None
|
|
overwrite
|
allow overwriting existing out-of-memory table. |
False
|
Returns:
| Type | Description |
|---|---|
|
new table with chromatograms and chromatogram boundaries. |
RunFeatureFinderMetabo
¶
__call__(peak_map, ms_level=None, verbose=True, run_feature_grouper=True, split_by_precursors_mz_tol=0.0, **parameters)
¶
runs openms feature finder on peakmap.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
peak_map
|
emzed PeakMap object |
required | |
ms_level
|
ms level to pick peaks from, default picks from MS1 |
None
|
|
verbose
|
set to False to supress output |
True
|
|
run_feature_grouper
|
also run feature grouper from openms. |
True
|
|
split_by_precursors_mz_tol
|
ms2 peakmaps are split by precusor first. this
is the tolearance used for
PeakMap.split_by_precursors. Set to |
0.0
|