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SILACAnalyzer Class Reference

Algorithm to use for SILACAnalysis. More...

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

Inheritance diagram for SILACAnalyzer:
ProgressLogger

Public Member Functions

 SILACAnalyzer ()
 
void initialize (String selected_labels_, UInt charge_min_, UInt charge_max_, Int missed_cleavages_, UInt isotopes_per_peptide_min_, UInt isotopes_per_peptide_max_, DoubleReal rt_threshold_, DoubleReal rt_min_, DoubleReal intensity_cutoff_, DoubleReal intensity_correlation_, DoubleReal model_deviation_, bool allow_missing_peaks_, std::map< String, DoubleReal > label_identifiers)
 Initializes the algorithm with parameters. More...
 
void calculateLabelsAndMassShifts (std::map< String, DoubleReal > label_identifiers)
 Calculate the internal massShift and label datastructures from a map of identifiers and mass shifts (e.g. "Arg6" => 6.0201290268). More...
 
void run_all (MSExperiment< Peak1D > &exp, ConsensusMap &out_map)
 
PeakWidthEstimator::Result estimatePeakWidth (const MSExperiment< Peak1D > &exp)
 Peak width estimation. More...
 
void filterData (MSExperiment< Peak1D > &exp, const PeakWidthEstimator::Result &peak_width, std::vector< std::vector< SILACPattern > > &data)
 Filtering. More...
 
void clusterData (const MSExperiment<> &, const PeakWidthEstimator::Result &, std::vector< Clustering * > &, std::vector< std::vector< SILACPattern > > &data)
 Clustering. More...
 
std::vector< std::vector
< String > > & 
getSILAClabels ()
 Returns the list of SILAC labels, e.g. selected_labels="[Lys4,Arg6][Lys8,Arg10]" => SILAClabels[0][1]="Arg6". More...
 
std::vector< std::vector
< DoubleReal > > & 
getMassShifts ()
 Returns the list of mass shifts calcualted. More...
 
void generateClusterConsensusByCluster (ConsensusMap &, const Clustering &) const
 Generate ConsensusMap from clustering result. More...
 
void generateClusterConsensusByPattern (ConsensusMap &, const Clustering &, UInt &cluster_id) const
 Generate ConsensusMap from clustering result, one consensus per pattern. More...
 
void generateClusterDebug (std::ostream &out, const Clustering &clustering, UInt &cluster_id) const
 Generate debug output from clustering result. More...
 
void generateFilterConsensusByPattern (ConsensusMap &, const std::vector< SILACPattern > &) const
 Generate ConsensusMap from filter result. More...
 
void generateClusterFeatureByCluster (FeatureMap<> &, const Clustering &) const
 Generate FeatureMap from clustering result. More...
 
void readFilterConsensusByPattern (ConsensusMap &, std::vector< std::vector< SILACPattern > > &)
 Read filter result from ConsensusMap. More...
 
void readConsensus (const String &filename, ConsensusMap &in) const
 Read consensusXML from file to ConsensusMap. More...
 
void writeConsensus (const String &filename, ConsensusMap &out) const
 Write consensusXML from ConsensusMap to file. More...
 
void writeMzQuantML (const String &filename, MSQuantifications &msq) const
 Write MzQuantML from ConsensusMap to file. More...
 
void writeFeatures (const String &filename, FeatureMap<> &out) const
 Write featureXML from FeatureMap to file. More...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. 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...
 

Static Public Member Functions

static const StringselectColor (UInt nr)
 

Private Types

typedef SILACClustering Clustering
 

Private Member Functions

ConsensusFeature generateSingleConsensusByPattern (const SILACPattern &) const
 Generate a consensus entry from a pattern. More...
 

Private Attributes

String in
 
String out
 
String out_clusters
 
String out_features
 
String out_mzq
 
String out_filters
 
String in_filters
 
String out_debug
 
String selected_labels
 
UInt charge_min
 
UInt charge_max
 
Int missed_cleavages
 
UInt isotopes_per_peptide_min
 
UInt isotopes_per_peptide_max
 
DoubleReal rt_threshold
 
DoubleReal rt_min
 
DoubleReal intensity_cutoff
 
DoubleReal intensity_correlation
 
DoubleReal model_deviation
 
bool allow_missing_peaks
 
std::vector< std::vector
< String > > 
SILAClabels
 
std::vector< std::vector
< DoubleReal > > 
massShifts
 
MSQuantifications msq
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
SignedSize begin_
 
SignedSize end_
 
SignedSize value_
 
QProgressDialog * dlg_
 
StopWatch stop_watch_
 
time_t last_invoke_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

Algorithm to use for SILACAnalysis.

Please initialize before usage using the initialize function. Next, one can estimate the peak width before filtering the data.

In the final step, clusterData will generate the output data.

See Also
SILACFiltering

Member Typedef Documentation

typedef SILACClustering Clustering
private

Constructor & Destructor Documentation

SILACAnalyzer ( )
inline

Member Function Documentation

void calculateLabelsAndMassShifts ( std::map< String, DoubleReal label_identifiers)

Calculate the internal massShift and label datastructures from a map of identifiers and mass shifts (e.g. "Arg6" => 6.0201290268).

Note that this part is necessary for the algorithm to work and this function is called from the initialize section. The algorithm has to be initialized _first_ with the list of actually used labels (selected_labels) using the initialize_sample call.

void clusterData ( const MSExperiment<> &  ,
const PeakWidthEstimator::Result ,
std::vector< Clustering * > &  ,
std::vector< std::vector< SILACPattern > > &  data 
)

Clustering.

PeakWidthEstimator::Result estimatePeakWidth ( const MSExperiment< Peak1D > &  exp)

Peak width estimation.

void filterData ( MSExperiment< Peak1D > &  exp,
const PeakWidthEstimator::Result peak_width,
std::vector< std::vector< SILACPattern > > &  data 
)

Filtering.

void generateClusterConsensusByCluster ( ConsensusMap ,
const Clustering  
) const

Generate ConsensusMap from clustering result.

void generateClusterConsensusByPattern ( ConsensusMap ,
const Clustering ,
UInt cluster_id 
) const

Generate ConsensusMap from clustering result, one consensus per pattern.

void generateClusterDebug ( std::ostream &  out,
const Clustering clustering,
UInt cluster_id 
) const

Generate debug output from clustering result.

void generateClusterFeatureByCluster ( FeatureMap<> &  ,
const Clustering  
) const

Generate FeatureMap from clustering result.

void generateFilterConsensusByPattern ( ConsensusMap ,
const std::vector< SILACPattern > &   
) const

Generate ConsensusMap from filter result.

ConsensusFeature generateSingleConsensusByPattern ( const SILACPattern ) const
private

Generate a consensus entry from a pattern.

std::vector<std::vector<DoubleReal> >& getMassShifts ( )
inline

Returns the list of mass shifts calcualted.

std::vector<std::vector<String> >& getSILAClabels ( )
inline

Returns the list of SILAC labels, e.g. selected_labels="[Lys4,Arg6][Lys8,Arg10]" => SILAClabels[0][1]="Arg6".

void initialize ( String  selected_labels_,
UInt  charge_min_,
UInt  charge_max_,
Int  missed_cleavages_,
UInt  isotopes_per_peptide_min_,
UInt  isotopes_per_peptide_max_,
DoubleReal  rt_threshold_,
DoubleReal  rt_min_,
DoubleReal  intensity_cutoff_,
DoubleReal  intensity_correlation_,
DoubleReal  model_deviation_,
bool  allow_missing_peaks_,
std::map< String, DoubleReal label_identifiers 
)
inline

Initializes the algorithm with parameters.

Parameters
selected_labels_Labels used for labelling the sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. The used labels must be described in the label_identifiers parameter
label_identifiersa map of labels and corresponding mass shits e.g. "Arg6" => 6.0201290268
void readConsensus ( const String filename,
ConsensusMap in 
) const
inline

Read consensusXML from file to ConsensusMap.

References ConsensusXMLFile::load().

void readFilterConsensusByPattern ( ConsensusMap ,
std::vector< std::vector< SILACPattern > > &   
)

Read filter result from ConsensusMap.

void run_all ( MSExperiment< Peak1D > &  exp,
ConsensusMap out_map 
)
inline
static const String& selectColor ( UInt  nr)
static
void writeConsensus ( const String filename,
ConsensusMap out 
) const
inline
void writeFeatures ( const String filename,
FeatureMap<> &  out 
) const
inline
void writeMzQuantML ( const String filename,
MSQuantifications msq 
) const
inline

Write MzQuantML from ConsensusMap to file.

References MzQuantMLFile::store().

Member Data Documentation

bool allow_missing_peaks
private
UInt charge_max
private
UInt charge_min
private
String in
private
String in_filters
private
DoubleReal intensity_correlation
private
DoubleReal intensity_cutoff
private
UInt isotopes_per_peptide_max
private
UInt isotopes_per_peptide_min
private
std::vector<std::vector<DoubleReal> > massShifts
private
Int missed_cleavages
private
DoubleReal model_deviation
private
MSQuantifications msq
private
String out
private
String out_clusters
private
String out_debug
private
String out_features
private
String out_filters
private
String out_mzq
private
DoubleReal rt_min
private
DoubleReal rt_threshold
private
String selected_labels
private
std::vector<std::vector<String> > SILAClabels
private

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5