OpenMS
2.8.0
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A container type that gathers peaks similar in m/z and moving along retention time. More...
#include <OpenMS/KERNEL/MassTrace.h>
Public Types | |
enum | MT_QUANTMETHOD { MT_QUANT_AREA = 0 , MT_QUANT_MEDIAN , MT_QUANT_HEIGHT , SIZE_OF_MT_QUANTMETHOD } |
Public Member Functions | |
Constructors and Destructor | |
MassTrace ()=default | |
Default constructor. More... | |
MassTrace (const std::list< PeakType > &trace_peaks) | |
MassTrace (const std::vector< PeakType > &trace_peaks) | |
Detailed constructor for vector. More... | |
~MassTrace ()=default | |
Destructor. More... | |
MassTrace (const MassTrace &)=default | |
Copy constructor. More... | |
MassTrace & | operator= (const MassTrace &)=default |
Assignment operator. More... | |
PeakType & | operator[] (const Size &mt_idx) |
Random access operator. More... | |
const PeakType & | operator[] (const Size &mt_idx) const |
Accessor methods | |
Size | getSize () const |
Returns the number of peaks contained in the mass trace. More... | |
String | getLabel () const |
Gets label of mass trace. More... | |
void | setLabel (const String &label) |
Sets label of mass trace. More... | |
double | getCentroidMZ () const |
Returns the centroid m/z. More... | |
double | getCentroidRT () const |
Returns the centroid RT. More... | |
double | getCentroidSD () const |
void | setCentroidSD (const double &tmp_sd) |
double | getFWHM () const |
double | getTraceLength () const |
Returns the length of the trace (as difference in RT) More... | |
std::pair< Size, Size > | getFWHMborders () const |
const std::vector< double > & | getSmoothedIntensities () const |
Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!). More... | |
void | setSmoothedIntensities (const std::vector< double > &db_vec) |
Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing). More... | |
double | getAverageMS1CycleTime () const |
Get average scan time of mass trace. More... | |
Computational methods | |
double | computeSmoothedPeakArea () const |
Sum all non-negative (smoothed!) intensities in the mass trace. More... | |
double | computePeakArea () const |
Sum intensities of all peaks in the mass trace. More... | |
Size | findMaxByIntPeak (bool use_smoothed_ints=false) const |
Return the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities). More... | |
double | estimateFWHM (bool use_smoothed_ints=false) |
void | setQuantMethod (MT_QUANTMETHOD method) |
determine if area or median is used for quantification More... | |
MT_QUANTMETHOD | getQuantMethod () const |
check if area or median is used for quantification More... | |
double | computeFwhmAreaSmooth () const |
Compute chromatographic peak area within the FWHM range. More... | |
double | computeFwhmArea () const |
double | getIntensity (bool smoothed) const |
double | getMaxIntensity (bool smoothed) const |
ConvexHull2D | getConvexhull () const |
Return the mass trace's convex hull. More... | |
Update methods for centroid RT and m/z | |
void | updateSmoothedMaxRT () |
void | updateWeightedMeanRT () |
Compute & update centroid RT as a intensity-weighted mean of RTs. More... | |
void | updateSmoothedWeightedMeanRT () |
void | updateMedianRT () |
Compute & update centroid RT as median position of intensities. More... | |
void | updateMedianMZ () |
Compute & update centroid m/z as median of m/z values. More... | |
void | updateMeanMZ () |
Compute & update centroid m/z as mean of m/z values. More... | |
void | updateWeightedMeanMZ () |
Compute & update centroid m/z as weighted mean of m/z values. More... | |
void | updateWeightedMZsd () |
Compute & update m/z standard deviation of mass trace as weighted mean of m/z values. More... | |
Static Public Member Functions | |
static MT_QUANTMETHOD | getQuantMethod (const String &val) |
converts a string to enum value; returns 'SIZE_OF_MT_QUANTMETHOD' upon error More... | |
Public Attributes | |
double | fwhm_mz_avg = 0 |
Average FWHM of m/z peaks. More... | |
Static Public Attributes | |
static const std::string | names_of_quantmethod [SIZE_OF_MT_QUANTMETHOD] |
Private Member Functions | |
double | computeMedianIntensity_ () const |
median of trace intensities More... | |
double | linearInterpolationAtY_ (double xA, double xB, double yA, double yB, double y_eval) const |
Private Attributes | |
std::vector< PeakType > | trace_peaks_ |
Actual MassTrace container for doing centroid calculation, peak width estimation etc. More... | |
double | centroid_mz_ = 0.0 |
Centroid m/z. More... | |
double | centroid_sd_ = 0.0 |
intensity-weighted STD More... | |
double | centroid_rt_ = 0.0 |
Centroid RT. More... | |
String | label_ |
Trace label. More... | |
std::vector< double > | smoothed_intensities_ |
Container for smoothed intensities. Smoothing must be done externally. More... | |
double | fwhm_ = 0.0 |
FWHM of RT peak. More... | |
Size | fwhm_start_idx_ = 0 |
index into 'trace_peaks_' vector (inclusive) More... | |
Size | fwhm_end_idx_ = 0 |
index into 'trace_peaks_' vector (inclusive) More... | |
MT_QUANTMETHOD | quant_method_ = MT_QUANT_AREA |
use area under mass trace or the median of intensities More... | |
Iterators | |
typedef std::vector< PeakType >::iterator | iterator |
typedef std::vector< PeakType >::const_iterator | const_iterator |
typedef std::vector< PeakType >::reverse_iterator | reverse_iterator |
typedef std::vector< PeakType >::const_reverse_iterator | const_reverse_iterator |
iterator | begin () |
iterator | end () |
const_iterator | begin () const |
const_iterator | end () const |
reverse_iterator | rbegin () |
reverse_iterator | rend () |
const_reverse_iterator | rbegin () const |
const_reverse_iterator | rend () const |
A container type that gathers peaks similar in m/z and moving along retention time.
Depending on the method of extraction a mass trace could virtually represent a complete extracted ion chromatogram (XIC) or merely a part of it (e.g., a chromatographic peak). The kernel class provides methods for computing mass trace characteristics such as its centroid m/z and retention time. Coeluting mass traces can be further assembled to complete isotope patterns of peptides/metabolites.
typedef std::vector<PeakType>::const_iterator const_iterator |
typedef std::vector<PeakType>::const_reverse_iterator const_reverse_iterator |
typedef std::vector<PeakType>::reverse_iterator reverse_iterator |
enum MT_QUANTMETHOD |
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Default constructor.
Detailed constructor (useful, since Mass Traces are commonly assembled by prepending and appending – which is faster using lists)
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Destructor.
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double computeFwhmArea | ( | ) | const |
double computeFwhmAreaSmooth | ( | ) | const |
Compute chromatographic peak area within the FWHM range.
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median of trace intensities
double computePeakArea | ( | ) | const |
Sum intensities of all peaks in the mass trace.
double computeSmoothedPeakArea | ( | ) | const |
Sum all non-negative (smoothed!) intensities in the mass trace.
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double estimateFWHM | ( | bool | use_smoothed_ints = false | ) |
Size findMaxByIntPeak | ( | bool | use_smoothed_ints = false | ) | const |
Return the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities).
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Get average scan time of mass trace.
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Returns the centroid m/z.
Referenced by CmpMassTraceByMZ::operator()().
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Returns the centroid RT.
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ConvexHull2D getConvexhull | ( | ) | const |
Return the mass trace's convex hull.
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double getIntensity | ( | bool | smoothed | ) | const |
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Gets label of mass trace.
double getMaxIntensity | ( | bool | smoothed | ) | const |
MT_QUANTMETHOD getQuantMethod | ( | ) | const |
check if area or median is used for quantification
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converts a string to enum value; returns 'SIZE_OF_MT_QUANTMETHOD' upon error
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Returns the number of peaks contained in the mass trace.
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Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!).
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Returns the length of the trace (as difference in RT)
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calculate x coordinate of start/end indexes at half_max calculation is based on (yB - yA) / (xB - xA) = (y_eval - yA) / (xC - xA) solve for xC: xC = xA + ((y_eval - yA) * (xB - xA) / (yB - yA))
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Sets label of mass trace.
void setQuantMethod | ( | MT_QUANTMETHOD | method | ) |
determine if area or median is used for quantification
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Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing).
void updateMeanMZ | ( | ) |
Compute & update centroid m/z as mean of m/z values.
void updateMedianMZ | ( | ) |
Compute & update centroid m/z as median of m/z values.
void updateMedianRT | ( | ) |
Compute & update centroid RT as median position of intensities.
void updateSmoothedMaxRT | ( | ) |
void updateSmoothedWeightedMeanRT | ( | ) |
void updateWeightedMeanMZ | ( | ) |
Compute & update centroid m/z as weighted mean of m/z values.
void updateWeightedMeanRT | ( | ) |
Compute & update centroid RT as a intensity-weighted mean of RTs.
void updateWeightedMZsd | ( | ) |
Compute & update m/z standard deviation of mass trace as weighted mean of m/z values.
Make sure to call update(Weighted)(Mean|Median)MZ() first!
use getCentroidSD() to get result
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Centroid m/z.
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Centroid RT.
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intensity-weighted STD
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FWHM of RT peak.
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index into 'trace_peaks_' vector (inclusive)
double fwhm_mz_avg = 0 |
Average FWHM of m/z peaks.
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index into 'trace_peaks_' vector (inclusive)
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Trace label.
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use area under mass trace or the median of intensities
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Container for smoothed intensities. Smoothing must be done externally.