[experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map More...
#include <OpenMS/ANALYSIS/QUANTITATION/ItraqChannelExtractor.h>
 
  
 | Public Types | |
| typedef ItraqConstants::ChannelMapType | ChannelMapType | 
|  Public Types inherited from ItraqConstants | |
| enum | ITRAQ_TYPES { FOURPLEX = 0, EIGHTPLEX, TMT_SIXPLEX, SIZE_OF_ITRAQ_TYPES } | 
| typedef Map< Int, ChannelInfo > | ChannelMapType | 
| maps iTRAQ channel (e.g. 117) to more information  More... | |
| typedef std::vector< Matrix < double > > | IsotopeMatrices | 
| (user defined?) isotope correction matrix in (-2, -1, +1, +2) row style  More... | |
| Public Member Functions | |
| ItraqChannelExtractor () | |
| Constructor (assuming 4plex)  More... | |
| ItraqChannelExtractor (Int itraq_type) | |
| Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES)  More... | |
| ItraqChannelExtractor (Int itraq_type, const Param ¶m) | |
| Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) and param.  More... | |
| ItraqChannelExtractor (const ItraqChannelExtractor &cp) | |
| copy constructor  More... | |
| ItraqChannelExtractor & | operator= (const ItraqChannelExtractor &rhs) | 
| assignment operator  More... | |
| void | run (const MSExperiment< Peak1D > &ms_exp_data, ConsensusMap &consensus_map) | 
| extracts the iTRAQ channels from the tandem MS data and stores intensity values in a consensus map  More... | |
|  Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages.  More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor.  More... | |
| virtual | ~DefaultParamHandler () | 
| Destructor.  More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
| Protected Member Functions | |
| void | setDefaultParams_ () | 
| void | updateMembers_ () | 
| implemented for DefaultParamHandler  More... | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
| Private Member Functions | |
| void | init_ () | 
| initialize  More... | |
| Private Attributes | |
| Int | itraq_type_ | 
| set to either ItraqConstants::FOURPLEX, ItraqConstants::EIGHTPLEX, or ItraqConstants::TMT_SIXPLEX  More... | |
| ChannelMapType | channel_map_ | 
| Additional Inherited Members | |
|  Static Public Member Functions inherited from ItraqConstants | |
| static StringList | getIsotopeMatrixAsStringList (const int itraq_type, const IsotopeMatrices &isotope_corrections) | 
| convert isotope correction matrix to stringlist  More... | |
| static void | updateIsotopeMatrixFromStringList (const int itraq_type, const StringList &channels, IsotopeMatrices &isotope_corrections) | 
| convert strings to isotope correction matrix rows  More... | |
| static void | initChannelMap (const int itraq_type, ChannelMapType &map) | 
| information about an iTRAQ channel  More... | |
| static void | updateChannelMap (const StringList &active_channels, ChannelMapType &map) | 
| activate & annotate channels  More... | |
| static Matrix< double > | translateIsotopeMatrix (const int &itraq_type, const IsotopeMatrices &isotope_corrections) | 
| translate isotope correction matrix in -2,-1,+1,+2 form into 114,115,116,117 format  More... | |
|  Static Public Attributes inherited from ItraqConstants | |
| static const Int | CHANNEL_COUNT [] | 
| static const Int | CHANNELS_FOURPLEX [4][1] | 
| channel names for 4plex( 114, 115, 116, 117)  More... | |
| static const Int | CHANNELS_EIGHTPLEX [8][1] | 
| channel names for 8plex( 113, 114, 115, 116, 117, 118, 119, 121)  More... | |
| static const Int | CHANNELS_TMT_SIXPLEX [6][1] | 
| channel names for 6plex TMT with CID fragmentation( 126, 127, 128, 129, 130, 131)  More... | |
| static const double | ISOTOPECORRECTIONS_FOURPLEX [4][4] | 
| default isotope correction matrix (4 plex)  More... | |
| static const double | ISOTOPECORRECTIONS_EIGHTPLEX [8][4] | 
| default isotope correction matrix (8 plex)  More... | |
| static const double | ISOTOPECORRECTIONS_TMT_SIXPLEX [6][4] | 
| default isotope correction matrix (6 plex TMT)  More... | |
|  Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ | 
| Container for current parameters.  More... | |
| Param | defaults_ | 
| Container for default parameters. This member should be filled in the constructor of derived classes!  More... | |
| std::vector< String > | subsections_ | 
| Container for registered subsections. This member should be filled in the constructor of derived classes!  More... | |
| String | error_name_ | 
| Name that is displayed in error messages during the parameter checking.  More... | |
| bool | check_defaults_ | 
| If this member is set to false no checking if parameters in done;.  More... | |
| bool | warn_empty_defaults_ | 
| If this member is set to false no warning is emitted when defaults are empty;.  More... | |
[experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map
[experimental class] This class supports 4 and 8 channel iTRAQ and 6 channel TMT and will optionally do peak picking before the quantitation step. Quantitation is done by adding all signals within a small delta around the expected m/z of each channel. When all channels are found to be empty, the ConsensusFeature is not created. No postprocessing is done here. Use ItraqQuantifier for that!
Parameters of this class are:| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| select_activation | string | High-energy collision-induced dissociation | Collision-induced dissociation, Post-source decay, Plasma desorption, Surface-induced dissociation, Blackbody infrared radiative dissociation, Electron capture dissociation, Infrared multiphoton dissociation, Sustained off-resonance irradiation, High-energy collision-induced dissociation, Low-energy collision-induced dissociation, Photodissociation, Electron transfer dissociation, | Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering. | 
| reporter_mass_shift | float | 0.1 | min: 1e-08 max: 0.5 | Allowed shift (left to right) in Da from the expected position. | 
| channel_active | string list | [114:liver, 117:lung] | Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex) in format | 
Constructor (assuming 4plex)
| 
 | explicit | 
Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES)
| ItraqChannelExtractor | ( | Int | itraq_type, | 
| const Param & | param | ||
| ) | 
Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) and param.
| ItraqChannelExtractor | ( | const ItraqChannelExtractor & | cp | ) | 
copy constructor
| 
 | private | 
initialize
| ItraqChannelExtractor& operator= | ( | const ItraqChannelExtractor & | rhs | ) | 
assignment operator
| void run | ( | const MSExperiment< Peak1D > & | ms_exp_data, | 
| ConsensusMap & | consensus_map | ||
| ) | 
extracts the iTRAQ channels from the tandem MS data and stores intensity values in a consensus map
| ms_exp_data | Raw data to read | 
| consensus_map | 
| 
 | protected | 
| 
 | protectedvirtual | 
implemented for DefaultParamHandler
Reimplemented from DefaultParamHandler.
| 
 | private | 
map the channel-name (eg 114) onto its description and the centroid mass the channel-name is also the id-string in the mapList section of the ConsensusMap
| 
 | private | 
set to either ItraqConstants::FOURPLEX, ItraqConstants::EIGHTPLEX, or ItraqConstants::TMT_SIXPLEX
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |