A helper class that is used by several OpenSWATH tools. More...
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h>
Static Public Member Functions | |
static void | selectSwathTransitions (const OpenMS::TargetedExperiment &targeted_exp, OpenMS::TargetedExperiment &transition_exp_used, 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 &transition_exp_used, 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::MSExperiment< Peak1D > &swath_map, double &lower, double &upper) |
Get the lower / upper offset for this SWATH map and do some sanity checks. More... | |
template<class TargetedExperimentT > | |
static bool | checkSwathMapAndSelectTransitions (const OpenMS::MSExperiment< Peak1D > &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &transition_exp_used, double min_upper_edge_dist) |
Check the map and select transition in one function. More... | |
static std::pair< double, double > | estimateRTRange (OpenSwath::LightTargetedExperiment &exp) |
Estimate the retention time span of a targeted experiment (returns min/max values as a pair) More... | |
static std::map< std::string, double > | simpleFindBestFeature (OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &transition_group_map, bool useQualCutoff=false, double qualCutoff=0.0) |
Simple method to extract the best Feature for each transition group (e.g. for RT alignment) More... | |
A helper class that is used by several OpenSWATH tools.
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static |
Get the lower / upper offset for this SWATH map and do some sanity checks.
Sanity check for the whole map:
throws | IllegalArgument exception if the sanity checks fail. |
Referenced by OpenSwathHelper::checkSwathMapAndSelectTransitions(), and SwathFile::loadSplit().
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inlinestatic |
Check the map and select transition in one function.
References OpenSwathHelper::checkSwathMap(), DocumentIdentifier::getLoadedFilePath(), OpenSwathHelper::selectSwathTransitions(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
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static |
Estimate the retention time span of a targeted experiment (returns min/max values as a pair)
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static |
Select transitions between lower and upper and write them into the new TargetedExperiment.
Version for the OpenMS TargetedExperiment
Referenced by OpenSwathHelper::checkSwathMapAndSelectTransitions(), OpenSwathWorkflow::performExtraction(), and OpenSwathWorkflow::simpleExtractChromatograms().
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static |
Select transitions between lower and upper and write them into the new TargetedExperiment.
Version for the LightTargetedExperiment
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static |
Simple method to extract the best Feature for each transition group (e.g. for RT alignment)
transition_group_map | Input data |
pairs | Output (containing pairs of mapping data |
Referenced by OpenSwathWorkflow::RTNormalization().
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:44 using doxygen 1.8.5 |