FeatureHypothesis Class Reference

Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis). More...

#include <OpenMS/FILTERING/DATAREDUCTION/FeatureFindingMetabo.h>

Collaboration diagram for FeatureHypothesis:

Public Member Functions

 FeatureHypothesis ()=default
 default constructor More...
 ~FeatureHypothesis ()=default
 default destructor More...
 FeatureHypothesis (const FeatureHypothesis &)=default
 copy constructor More...
FeatureHypothesisoperator= (const FeatureHypothesis &rhs)=default
 assignment operator More...
Size getSize () const
String getLabel () const
std::vector< StringgetLabels () const
double getScore () const
void setScore (const double &score)
SignedSize getCharge () const
void setCharge (const SignedSize &ch)
std::vector< double > getAllIntensities (bool smoothed=false) const
std::vector< double > getAllCentroidMZ () const
std::vector< double > getAllCentroidRT () const
std::vector< double > getIsotopeDistances () const
double getCentroidMZ () const
double getCentroidRT () const
double getFWHM () const
void addMassTrace (const MassTrace &)
 addMassTrace More...
double getMonoisotopicFeatureIntensity (bool) const
double getSummedFeatureIntensity (bool) const
double getMaxIntensity (bool smoothed=false) const
 return highest apex of all isotope traces More...
Size getNumFeatPoints () const
std::vector< ConvexHull2DgetConvexHulls () const
std::vector< OpenMS::MSChromatogramgetChromatograms (UInt64 feature_id) const

Private Attributes

std::vector< const MassTrace * > iso_pattern_
double feat_score_ {}
SignedSize charge_ {}

Detailed Description

Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis).

Parameters of this class are:

local_rt_range float10.0  RT range where to look for coeluting mass traces
local_mz_range float6.5  MZ range where to look for isotopic mass traces
charge_lower_bound int1  Lowest charge state to consider
charge_upper_bound int3  Highest charge state to consider
chrom_fwhm float5.0  Expected chromatographic peak width (in seconds).
report_summed_ints stringfalse false, trueSet to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone.
enable_RT_filtering stringtrue false, trueRequire sufficient overlap in RT while assembling mass traces. Disable for direct injection data..
isotope_filtering_model stringmetabolites (5% RMS) metabolites (2% RMS), metabolites (5% RMS), peptides, noneRemove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device.
mz_scoring_13C stringfalse false, trueUse the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, MCP.).
use_smoothed_intensities stringtrue false, trueUse LOWESS intensities instead of raw intensities.
report_convex_hulls stringfalse false, trueAugment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably).
report_chromatograms stringfalse false, trueAdds Chromatogram for each reported feature (Output in mzml).
remove_single_traces stringfalse false, trueRemove unassembled traces (single traces).
mz_scoring_by_elements stringfalse false, trueUse the m/z range of the assumed elements to detect isotope peaks. A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'
elements stringCHNOPS  Elements assumes to be present in the sample (this influences isotope detection).

  • If a section name is documented, the documentation is displayed as tooltip.
  • Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ FeatureHypothesis() [1/2]

FeatureHypothesis ( )

default constructor

◆ ~FeatureHypothesis()

~FeatureHypothesis ( )

default destructor

◆ FeatureHypothesis() [2/2]

FeatureHypothesis ( const FeatureHypothesis )

copy constructor

Member Function Documentation

◆ addMassTrace()

void addMassTrace ( const MassTrace )


◆ getAllCentroidMZ()

std::vector<double> getAllCentroidMZ ( ) const

◆ getAllCentroidRT()

std::vector<double> getAllCentroidRT ( ) const

◆ getAllIntensities()

std::vector<double> getAllIntensities ( bool  smoothed = false) const

◆ getCentroidMZ()

double getCentroidMZ ( ) const

◆ getCentroidRT()

double getCentroidRT ( ) const

◆ getCharge()

SignedSize getCharge ( ) const

◆ getChromatograms()

std::vector< OpenMS::MSChromatogram > getChromatograms ( UInt64  feature_id) const

◆ getConvexHulls()

std::vector<ConvexHull2D> getConvexHulls ( ) const

◆ getFWHM()

double getFWHM ( ) const

◆ getIsotopeDistances()

std::vector<double> getIsotopeDistances ( ) const

◆ getLabel()

String getLabel ( ) const

◆ getLabels()

std::vector<String> getLabels ( ) const

◆ getMaxIntensity()

double getMaxIntensity ( bool  smoothed = false) const

return highest apex of all isotope traces

◆ getMonoisotopicFeatureIntensity()

double getMonoisotopicFeatureIntensity ( bool  ) const

◆ getNumFeatPoints()

Size getNumFeatPoints ( ) const

◆ getScore()

double getScore ( ) const

◆ getSize()

Size getSize ( ) const

◆ getSummedFeatureIntensity()

double getSummedFeatureIntensity ( bool  ) const

◆ operator=()

FeatureHypothesis& operator= ( const FeatureHypothesis rhs)

assignment operator

◆ setCharge()

void setCharge ( const SignedSize ch)

◆ setScore()

void setScore ( const double &  score)

Member Data Documentation

◆ charge_

SignedSize charge_ {}

◆ feat_score_

double feat_score_ {}

◆ iso_pattern_

std::vector<const MassTrace*> iso_pattern_