[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 |
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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... | |
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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... | |
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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 | |
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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... | |
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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... | |
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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 post-processing is done here. Use ItraqQuantifier for that!
Constructor (assuming 4plex)
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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
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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 |
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protected |
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protectedvirtual |
implemented for DefaultParamHandler
Reimplemented from DefaultParamHandler.
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private |
map the channel-name (e.g. 114) onto its description and the centroid mass the channel-name is also the id-string in the mapList section of the ConsensusMap
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private |
set to either ItraqConstants::FOURPLEX, ItraqConstants::EIGHTPLEX, or ItraqConstants::TMT_SIXPLEX
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 12:49:28 using doxygen 1.8.11 |