Algorithm to use for SILACAnalysis. More...
#include <OpenMS/FILTERING/DATAREDUCTION/SILACAnalyzer.h>
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... | |
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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 String & | selectColor (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 | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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LogType | type_ |
SignedSize | begin_ |
SignedSize | end_ |
SignedSize | value_ |
QProgressDialog * | dlg_ |
StopWatch | stop_watch_ |
time_t | last_invoke_ |
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static int | recursion_depth_ |
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.
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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.
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Generate a consensus entry from a pattern.
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Returns the list of mass shifts calcualted.
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Returns the list of SILAC labels, e.g. selected_labels="[Lys4,Arg6][Lys8,Arg10]" => SILAClabels[0][1]="Arg6".
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Initializes the algorithm with 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_identifiers | a map of labels and corresponding mass shits e.g. "Arg6" => 6.0201290268 |
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Read consensusXML from file to ConsensusMap.
References ConsensusXMLFile::load().
void readFilterConsensusByPattern | ( | ConsensusMap & | , |
std::vector< std::vector< SILACPattern > > & | |||
) |
Read filter result from ConsensusMap.
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Write consensusXML from ConsensusMap to file.
References ConsensusMap::applyMemberFunction(), ConsensusMap::setExperimentType(), UniqueIdInterface::setUniqueId(), ConsensusMap::sortByPosition(), and ConsensusXMLFile::store().
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Write featureXML from FeatureMap to file.
References FeatureMap< FeatureT >::applyMemberFunction(), UniqueIdInterface::setUniqueId(), FeatureMap< FeatureT >::sortByPosition(), and FeatureXMLFile::store().
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Write MzQuantML from ConsensusMap to file.
References MzQuantMLFile::store().
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OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |