[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 |