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ItraqQuantifier Class Reference

Does post-processing on raw iTRAQ channel quantitation. More...

#include <OpenMS/ANALYSIS/QUANTITATION/ItraqQuantifier.h>

Inheritance diagram for ItraqQuantifier:
DefaultParamHandler ItraqConstants

Classes

struct  ItraqQuantifierStats
 Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) More...
 

Public Types

typedef ItraqConstants::ChannelInfo ChannelInfo
 
typedef ItraqConstants::ChannelMapType ChannelMapType
 
typedef ItraqConstants::IsotopeMatrices IsotopeMatrices
 
- Public Types inherited from ItraqConstants
enum  ITRAQ_TYPES { FOURPLEX = 0, EIGHTPLEX, TMT_SIXPLEX, SIZE_OF_ITRAQ_TYPES }
 
typedef Map< Int, ChannelInfoChannelMapType
 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

 ItraqQuantifier ()
 Constructor (assuming 4-plex experiment) More...
 
 ItraqQuantifier (Int itraq_type)
 Constructor with iTRAQ-type (either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX) More...
 
 ItraqQuantifier (Int itraq_type, const Param &param)
 Constructor with iTRAQ-type (either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX) and Param. More...
 
 ItraqQuantifier (const ItraqQuantifier &cp)
 copy constructor More...
 
ItraqQuantifieroperator= (const ItraqQuantifier &rhs)
 assignment operator More...
 
void run (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out)
 using the raw iTRAQ intensities we apply isotope correction, normalization (using median) More...
 
ItraqQuantifierStats getStats () const
 
- 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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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_ ()
 This method is used to update extra member variables at the end of the setParameters() method. 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 initIsotopeCorrections_ ()
 initialize More...
 
void reconstructChannelInfo_ (const ConsensusMap &consensus_map)
 
bool isIdentityCorrectionMatrix_ (const Matrix< double > &channel_frequency) const
 Check if the given channel_frequency matrix is an identity matrix. More...
 

Private Attributes

Int itraq_type_
 either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX More...
 
ChannelMapType channel_map_
 
IsotopeMatrices isotope_corrections_
 Matrices with isotope correction values (one for each plex-type) More...
 
ItraqQuantifierStats stats_
 stats for isotope correction More...
 

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< doubletranslateIsotopeMatrix (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< Stringsubsections_
 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...
 

Detailed Description

Does post-processing on raw iTRAQ channel quantitation.

Using the raw consensus map from ItraqChannelExtractor, a non-negative isotope correction, normalization (using median) and [optionally] protein inference is computed.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
isotope_correction stringtrue true, falseEnable isotope correction (highly recommended).
do_normalization stringfalse true, falseNormalize channels? Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!
channel_reference int114 min: 114 max: 117Number of the reference channel (114-117 for 4plex).
isotope_correction:4plex string list[114:0/1/5.9/0.2, 115:0/2/5.6/0.1, 116:0/3/4.5/0.1, 117:0.1/4/3.5/0.1]  Override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'.
isotope_correction:8plex string list[113:0/0/6.89/0.22, 114:0/0.94/5.9/0.16, 115:0/1.88/4.9/0.1, 116:0/2.82/3.9/0.07, 117:0.06/3.77/2.99/0, 118:0.09/4.71/1.88/0, 119:0.14/5.66/0.87/0, 121:0.27/7.44/0.18/0]  Override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'.

Note:

Member Typedef Documentation

Constructor & Destructor Documentation

Constructor (assuming 4-plex experiment)

ItraqQuantifier ( Int  itraq_type)
explicit

Constructor with iTRAQ-type (either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX)

ItraqQuantifier ( Int  itraq_type,
const Param param 
)

Constructor with iTRAQ-type (either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX) and Param.

copy constructor

Member Function Documentation

ItraqQuantifierStats getStats ( ) const
void initIsotopeCorrections_ ( )
private

initialize

bool isIdentityCorrectionMatrix_ ( const Matrix< double > &  channel_frequency) const
private

Check if the given channel_frequency matrix is an identity matrix.

Parameters
Thematrix to check.
ItraqQuantifier& operator= ( const ItraqQuantifier rhs)

assignment operator

void reconstructChannelInfo_ ( const ConsensusMap consensus_map)
private
void run ( const ConsensusMap consensus_map_in,
ConsensusMap consensus_map_out 
)

using the raw iTRAQ intensities we apply isotope correction, normalization (using median)

Parameters
consensus_map_inRaw iTRAQ intensities from previous step
consensus_map_outPost-processed iTRAQ ratios for peptides
Exceptions
Exception::FailedAPICallis least-squares fit fails
Exception::InvalidParameterif parameter is invalid (e.g. reference_channel)
void setDefaultParams_ ( )
protected
void updateMembers_ ( )
protectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

ChannelMapType channel_map_
private

map the channel-name (e.g., 114) onto its channel_info the channel-description is also the id-string in the mapList section of the ConsensusMap

IsotopeMatrices isotope_corrections_
private

Matrices with isotope correction values (one for each plex-type)

Int itraq_type_
private
ItraqQuantifierStats stats_
private

stats for isotope correction


OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:02 using doxygen 1.8.9.1