OpenMS
2.5.0
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A helper class that is used by several OpenSWATH tools. More...
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h>
Static Public Member Functions | |
static String | computePrecursorId (const String &transition_group_id, int isotope) |
Compute unique precursor identifier. More... | |
static String | computeTransitionGroupId (const String &precursor_id) |
Compute transition group id. More... | |
static void | selectSwathTransitions (const OpenMS::TargetedExperiment &targeted_exp, OpenMS::TargetedExperiment &selected_transitions, double min_upper_edge_dist, double lower, double upper) |
Select transitions between lower and upper and write them into the new TargetedExperiment. More... | |
static void | selectSwathTransitions (const OpenSwath::LightTargetedExperiment &targeted_exp, OpenSwath::LightTargetedExperiment &selected_transitions, double min_upper_edge_dist, double lower, double upper) |
Select transitions between lower and upper and write them into the new TargetedExperiment. More... | |
static void | checkSwathMap (const OpenMS::PeakMap &swath_map, double &lower, double &upper, double ¢er) |
Get the lower / upper offset for this SWATH map and do some sanity checks. More... | |
template<class TargetedExperimentT > | |
static bool | checkSwathMapAndSelectTransitions (const OpenMS::PeakMap &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &selected_transitions, double min_upper_edge_dist) |
Check the map and select transition in one function. More... | |
static std::pair< double, double > | estimateRTRange (const OpenSwath::LightTargetedExperiment &exp) |
Computes the min and max retention time value. More... | |
static std::map< std::string, double > | simpleFindBestFeature (const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &transition_group_map, bool useQualCutoff=false, double qualCutoff=0.0) |
Returns the feature with the highest score for each transition group. More... | |
A helper class that is used by several OpenSWATH tools.
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Get the lower / upper offset for this SWATH map and do some sanity checks.
Sanity check for the whole map:
[in] | swath_map | Input SWATH map to check |
[in] | lower | Lower edge of SWATH window (in Th) |
[in] | upper | Upper edge of SWATH window (in Th) |
throws | IllegalArgument exception if the sanity checks fail. |
Referenced by OpenSwathHelper::checkSwathMapAndSelectTransitions().
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inlinestatic |
Check the map and select transition in one function.
Computes lower and upper offset for the SWATH map and performs some sanity checks (see checkSwathMap()). Then selects transitions.
[in] | exp | Input SWATH map to check |
[in] | targeted_exp | Transition list for selection |
[out] | selected_transitions | Selected transitions for SWATH window |
[in] | min_upper_edge_dist | Distance in Th to the upper edge |
References OpenSwathHelper::checkSwathMap(), DocumentIdentifier::getLoadedFilePath(), OpenSwathHelper::selectSwathTransitions(), and MSExperiment::size().
Compute unique precursor identifier.
Uses transition_group_id and isotope number to compute a unique precursor id of the form "groupID_Precursor_ix" where x is the isotope number, e.g. the monoisotopic precursor would become "groupID_Precursor_i0".
[in] | transition_group_id | Unique id of the transition group (peptide/compound) |
[in] | isotope | Precursor isotope number |
Compute transition group id.
Uses the unique precursor identifier to compute the transition group id (peptide/compound identifier), reversing the operation performed by computePrecursorId().
[in] | precursor_id | Precursor identifier as computed by computePrecursorId() |
References OpenMS::Constants::k, String::prefix(), and String::split().
Referenced by ChromatogramExtractor::return_chromatogram().
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Computes the min and max retention time value.
Estimate the retention time span of a targeted experiment by returning the min/max values in retention time as a pair.
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Select transitions between lower and upper and write them into the new TargetedExperiment.
Version for the OpenMS TargetedExperiment
[in] | targeted_exp | Transition list for selection |
[out] | selected_transitions | Selected transitions for SWATH window |
[in] | min_upper_edge_dist | Distance in Th to the upper edge |
[in] | lower | Lower edge of SWATH window (in Th) |
[in] | upper | Upper edge of SWATH window (in Th) |
Referenced by OpenSwathHelper::checkSwathMapAndSelectTransitions().
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static |
Select transitions between lower and upper and write them into the new TargetedExperiment.
Version for the LightTargetedExperiment
[in] | targeted_exp | Transition list for selection |
[out] | selected_transitions | Selected transitions for SWATH window |
[in] | min_upper_edge_dist | Distance in Th to the upper edge |
[in] | lower | Lower edge of SWATH window (in Th) |
[in] | upper | Upper edge of SWATH window (in Th) |
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Returns the feature with the highest score for each transition group.
Simple method to extract the best feature for each transition group (e.g. for RT alignment). A quality cutoff can be used to skip some low-quality features altogether.
[in] | transition_group_map | Input data containing the picked and scored map |
useQualCutoff | Whether to apply a quality cutoff to the data | |
qualCutoff | What quality cutoff should be applied (all data above the cutoff will be kept) |