clusters results from multiplex filtering More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexClustering.h>
Inheritance diagram for MultiplexClustering:
Classes | |
| class | MultiplexDistance |
| scaled Euclidean distance for clustering More... | |
Public Types | |
| typedef GridBasedCluster::Point | Point |
| cluster centre, cluster bounding box, grid index More... | |
 Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. More... | |
Public Member Functions | |
| MultiplexClustering (const PeakMap &exp_profile, const PeakMap &exp_picked, const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > &boundaries, double rt_typical, double rt_minimum) | |
| constructor More... | |
| MultiplexClustering (const PeakMap &exp, double mz_tolerance, bool mz_tolerance_unit, double rt_typical, double rt_minimum) | |
| constructor More... | |
| std::vector< std::map< int, GridBasedCluster > > | cluster (const std::vector< MultiplexFilterResult > &filter_results) |
| cluster filter results Data points are grouped into clusters. Each cluster contains data about one peptide multiplet. More... | |
| Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| ~ProgressLogger () | |
| Destructor. More... | |
| ProgressLogger (const ProgressLogger &other) | |
| Copy constructor. More... | |
| ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More... | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More... | |
| LogType | getLogType () const |
| Returns the type of progress log being used. More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More... | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. More... | |
| void | endProgress () const |
| Ends the progress display. More... | |
Private Attributes | |
| std::vector< double > | grid_spacing_mz_ |
| grid spacing for clustering More... | |
| std::vector< double > | grid_spacing_rt_ |
| double | rt_scaling_ |
| scaling in y-direction for clustering More... | |
| double | rt_typical_ |
| typical retention time More... | |
| double | rt_minimum_ |
| minimum retention time More... | |
Additional Inherited Members | |
| Static Protected Member Functions inherited from ProgressLogger | |
| static String | logTypeToFactoryName_ (LogType type) |
| Return the name of the factory product used for this log type. More... | |
| Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| time_t | last_invoke_ |
| ProgressLoggerImpl * | current_logger_ |
| Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
Detailed Description
clusters results from multiplex filtering
The multiplex filtering algorithm identified regions in the picked and profile data that correspond to peptide features. This clustering algorithm takes these filter results as input and groups data points that belong to the same peptide features. It makes use of the general purpose hierarchical clustering implementation LocalClustering.
- See also
- MultiplexFiltering
- LocalClustering
Member Typedef Documentation
◆ Point
| typedef GridBasedCluster::Point Point |
cluster centre, cluster bounding box, grid index
Constructor & Destructor Documentation
◆ MultiplexClustering() [1/2]
| MultiplexClustering | ( | const PeakMap & | exp_profile, |
| const PeakMap & | exp_picked, | ||
| const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > & | boundaries, | ||
| double | rt_typical, | ||
| double | rt_minimum | ||
| ) |
constructor
- Parameters
-
exp_profile experimental data in profile mode exp_picked experimental data in centroid mode boundaries peak boundaries for exp_picked rt_typical elution time of a characteristic peptide in the sample rt_minimum shortest elution time i.e. all peptides appearing for a shorter time are being ignored
- Exceptions
-
Exception::IllegalArgument if centroided data and the corresponding list of peak boundaries do not contain same number of spectra
◆ MultiplexClustering() [2/2]
| MultiplexClustering | ( | const PeakMap & | exp, |
| double | mz_tolerance, | ||
| bool | mz_tolerance_unit, | ||
| double | rt_typical, | ||
| double | rt_minimum | ||
| ) |
constructor
- Parameters
-
exp experimental data in centroid mode mz_tolerance margin in m/z with which the centres of the same peak in different spectra my shift (or 'jitter') mz_tolerance_unit unit for mz_tolerance, ppm (true), Da (false) rt_typical elution time of a characteristic peptide in the sample rt_minimum shortest elution time i.e. all peptides appearing for a shorter time are being ignored
- Exceptions
-
Exception::IllegalArgument if centroided data and the corresponding list of peak boundaries do not contain same number of spectra
Member Function Documentation
◆ cluster()
| std::vector<std::map<int,GridBasedCluster> > cluster | ( | const std::vector< MultiplexFilterResult > & | filter_results | ) |
cluster filter results Data points are grouped into clusters. Each cluster contains data about one peptide multiplet.
- Parameters
-
filter_results data points relevant for peptide multiplets i.e. output from multiplex filtering
- Returns
- cluster results (cluster ID, details about cluster including list of filter result IDs belonging to the cluster)
Member Data Documentation
◆ grid_spacing_mz_
|
private |
grid spacing for clustering
◆ grid_spacing_rt_
|
private |
◆ rt_minimum_
|
private |
minimum retention time
◆ rt_scaling_
|
private |
scaling in y-direction for clustering
◆ rt_typical_
|
private |
typical retention time