| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
CalibrationData Class Reference

A helper class, holding all calibration points. More...

`#include <OpenMS/DATASTRUCTURES/CalibrationData.h>`

## Public Types

typedef RichPeak2D | CalDataType
typedef std::vector< CalDataType >::const_iterator | const_iterator
typedef std::vector< CalDataType >::value_type | value_type

## Public Member Functions

| CalibrationData ()
| Default constructor. More...
CalDataType::CoordinateType | getMZ (Size i) const
| Retrieve the observed m/z of the i'th calibration point. More...
CalDataType::CoordinateType | getRT (Size i) const
| Retrieve the observed RT of the i'th calibration point. More...
CalDataType::CoordinateType | getIntensity (Size i) const
| Retrieve the intensity of the i'th calibration point. More...
const_iterator | begin () const
| Begin iterator for calibration points. More...
const_iterator | end () const
| Past-the-end iterator for calibration points. More...
Size | size () const
| Number of calibration points. More...
bool | empty () const
| Do we have any calibration points. More...
void | clear ()
| Remove all calibration points. More...
void | setUsePPM (bool usePPM)
| When calling getError(), should ppm error or m/z error be returned? More...
bool | usePPM () const
| Current error unit (ppm or Th) More...
void | insertCalibrationPoint (CalDataType::CoordinateType rt, CalDataType::CoordinateType mz_obs, CalDataType::IntensityType intensity, CalDataType::CoordinateType mz_ref, double weight, int group=-1)
| Add a new calibration point. More...
Size | getNrOfGroups () const
| Number of peak groups (can be 0). More...
CalDataType::CoordinateType | getError (Size i) const
| Retrieve the error for i'th calibrant in either ppm or Th (depending on usePPM()) More...
CalDataType::CoordinateType | getRefMZ (Size i) const
| Retrieve the theoretical m/z of the i'th calibration point. More...
CalDataType::CoordinateType | getWeight (Size i) const
| Retrieve the weight of the i'th calibration point. More...
int | getGroup (Size i) const
| Retrieve the group of the i'th calibration point. More...
CalibrationData | median (double rt_left, double rt_right) const
| Compute the median in the given RT range for every peak group. More...
void | sortByRT ()
| Sort calibration points by RT, to allow for valid RT chunking. More...

## Static Public Member Functions

static StringList | getMetaValues ()
| List of meta-values which are used internally (for conversion to PeakMap). More...

## Private Attributes

std::vector< RichPeak2D > | data_
| calibration points More...
bool | use_ppm_
| return ppm values as y-values for the model instead of absolute delta in [Th] More...
std::set< int > | groups_
| peak groups present in this data More...

## Detailed Description

A helper class, holding all calibration points.

Calibration points can be filled from Peptide IDs (using FeatureMaps or vector<PeptideIds>) or from lock masses in Raw data (MSExperiment).

The m/z error can be queried using getError(). The unit of error is either ppm or Th, depending on usePPM().

Each calibration point can be assigned to a peak group. This should be done for calibration points derived from lock masses, to enable querying for a medianized representation of a lock mass trace in a certain RT range (see median()). For calibration points derived from peptide IDs, this does not make sense.

From this data, a calibration function can be computed (see MZTrafoModel class).

## Member Typedef Documentation

## ◆ CalDataType

typedef RichPeak2D CalDataType

## ◆ const_iterator

typedef std::vector<CalDataType>::const_iterator const_iterator

## ◆ value_type

typedef std::vector<CalDataType>::value_type value_type

## Constructor & Destructor Documentation

## ◆ CalibrationData()

CalibrationData | ( |  | ) |

Default constructor.

## Member Function Documentation

## ◆ begin()

const_iterator begin | ( |  | ) | const

Begin iterator for calibration points.

## ◆ clear()

void clear | ( |  | ) |

Remove all calibration points.

## ◆ empty()

bool empty | ( |  | ) | const

Do we have any calibration points.

## ◆ end()

const_iterator end | ( |  | ) | const

Past-the-end iterator for calibration points.

## ◆ getError()

CalDataType::CoordinateType getError | ( | Size | i | ) | const

Retrieve the error for i'th calibrant in either ppm or Th (depending on usePPM())

## ◆ getGroup()

int getGroup | ( | Size | i | ) | const

Retrieve the group of the i'th calibration point.

Parameters

  i | Index

Returns
  Group; returns -1 if peak has no group.

## ◆ getIntensity()

CalDataType::CoordinateType getIntensity | ( | Size | i | ) | const

Retrieve the intensity of the i'th calibration point.

## ◆ getMetaValues()

static StringList getMetaValues | ( |  | ) |

static

List of meta-values which are used internally (for conversion to PeakMap).

## ◆ getMZ()

CalDataType::CoordinateType getMZ | ( | Size | i | ) | const

Retrieve the observed m/z of the i'th calibration point.

## ◆ getNrOfGroups()

Size getNrOfGroups | ( |  | ) | const

Number of peak groups (can be 0).

## ◆ getRefMZ()

CalDataType::CoordinateType getRefMZ | ( | Size | i | ) | const

Retrieve the theoretical m/z of the i'th calibration point.

## ◆ getRT()

CalDataType::CoordinateType getRT | ( | Size | i | ) | const

Retrieve the observed RT of the i'th calibration point.

## ◆ getWeight()

CalDataType::CoordinateType getWeight | ( | Size | i | ) | const

Retrieve the weight of the i'th calibration point.

## ◆ insertCalibrationPoint()

void insertCalibrationPoint | ( | CalDataType::CoordinateType | rt,
|  | CalDataType::CoordinateType | mz_obs,
|  | CalDataType::IntensityType | intensity,
|  | CalDataType::CoordinateType | mz_ref,
|  | double | weight,
|  | int | group = `-1`
| ) |  |

Add a new calibration point.

Parameters

  rt | Retention time
  mz_obs | Observed m/z
  intensity | Intensity (useful for weighted model fitting)
  mz_ref | Theoretical m/z
  weight | Weight of calibration point (useful for weighted model fitting)
  group | Peak group of this calibration point. Using -1 will not assign any peak group. See also: median()

## ◆ median()

CalibrationData median | ( | double | rt_left,
|  | double | rt_right
| ) |  | const

Compute the median in the given RT range for every peak group.

This is usually applied on calibration data obtained from lock masses, where each lock mass has its own peak group. Median() then computes an 'medianized' observed(!) lock mass within a certain RT range and returns calibration data with one calibration point per group. Also intensity is 'medianized'. The theoretical m/z is expected to be identical for all calibration points in a peak group.

Groups must be specified during insertCalibrationPoint(). If no groups are present, the result is empty.

The container must be sorted by RT (see sortByRT())!

Parameters

  rt_left | Left border of RT range to medianize
  rt_right | Right border of RT range to medianize

Returns
  New container, containing median representation for each peak group

## ◆ setUsePPM()

void setUsePPM | ( | bool | usePPM | ) |

When calling getError(), should ppm error or m/z error be returned?

## ◆ size()

Size size | ( |  | ) | const

Number of calibration points.

Referenced by UTILProteomicsLFQ::recalibrateMasses_().

## ◆ sortByRT()

void sortByRT | ( |  | ) |

Sort calibration points by RT, to allow for valid RT chunking.

## ◆ usePPM()

bool usePPM | ( |  | ) | const

Current error unit (ppm or Th)

## Member Data Documentation

## ◆ data_

std::vector<RichPeak2D> data_

private

calibration points

## ◆ groups_

std::set<int> groups_

private

peak groups present in this data

## ◆ use_ppm_

bool use_ppm_

private

return ppm values as y-values for the model instead of absolute delta in [Th]