OpenMS: OpenSwathHelper Class Reference

| OpenMS 2.5.0

Static Public Member Functions | List of all members
OpenSwathHelper Class Reference

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 &center)
| 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...

## Detailed Description

A helper class that is used by several OpenSWATH tools.

## Member Function Documentation

## ◆ checkSwathMap()

static void checkSwathMap | ( | const OpenMS::PeakMap & | swath_map,
|  | double & | lower,
|  | double & | upper,
|  | double & | center
| ) |  |

static

Get the lower / upper offset for this SWATH map and do some sanity checks.

Sanity check for the whole map:

- all scans need to have exactly one precursor
- all scans need to have the same MS levels (otherwise extracting an XIC from them makes no sense)
- all scans need to have the same precursor isolation window (otherwise extracting an XIC from them makes no sense)

Parameters

  [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)

Exceptions

  throws | IllegalArgument exception if the sanity checks fail.

Referenced by OpenSwathHelper::checkSwathMapAndSelectTransitions().

## ◆ checkSwathMapAndSelectTransitions()

static bool checkSwathMapAndSelectTransitions | ( | const OpenMS::PeakMap & | exp,
|  | const TargetedExperimentT & | targeted_exp,
|  | TargetedExperimentT & | selected_transitions,
|  | double | min_upper_edge_dist
| ) |  |

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.

Parameters

  [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().

## ◆ computePrecursorId()

static String computePrecursorId | ( | const String & | transition_group_id,
|  | int | isotope
| ) |  |

inlinestatic

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".

Parameters

  [in] | transition_group_id | Unique id of the transition group (peptide/compound)
  [in] | isotope | Precursor isotope number

Returns
  Unique precursor identifier

## ◆ computeTransitionGroupId()

static String computeTransitionGroupId | ( | const String & | precursor_id | ) |

inlinestatic

Compute transition group id.

Uses the unique precursor identifier to compute the transition group id (peptide/compound identifier), reversing the operation performed by computePrecursorId().

Parameters

  [in] | precursor_id | Precursor identifier as computed by computePrecursorId()

Returns
  Original transition group id

References OpenMS::Constants::k, String::prefix(), and String::split().

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ estimateRTRange()

static std::pair<double,double> estimateRTRange | ( | const OpenSwath::LightTargetedExperiment & | exp | ) |

static

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.

Returns
  A std::pair that contains (min,max)

## ◆ selectSwathTransitions() [1/2]

static void selectSwathTransitions | ( | const OpenMS::TargetedExperiment & | targeted_exp,
|  | OpenMS::TargetedExperiment & | selected_transitions,
|  | double | min_upper_edge_dist,
|  | double | lower,
|  | double | upper
| ) |  |

static

Select transitions between lower and upper and write them into the new TargetedExperiment.

Version for the OpenMS TargetedExperiment

Parameters

  [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().

## ◆ selectSwathTransitions() [2/2]

static void selectSwathTransitions | ( | const OpenSwath::LightTargetedExperiment & | targeted_exp,
|  | OpenSwath::LightTargetedExperiment & | selected_transitions,
|  | double | min_upper_edge_dist,
|  | double | lower,
|  | double | upper
| ) |  |

static

Select transitions between lower and upper and write them into the new TargetedExperiment.

Version for the LightTargetedExperiment

Parameters

  [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)

## ◆ simpleFindBestFeature()

static std::map<std::string, double> simpleFindBestFeature | ( | const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType & | transition_group_map,
|  | bool | useQualCutoff = `false`,
|  | double | qualCutoff = `0.0`
| ) |  |

static

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.

Parameters

  [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)

Returns
  Result of the best scoring peaks (stored as map of peptide id and RT)