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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

List of all members.

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
 maps iTRAQ channel (e.g. 117) to more information
typedef
ItraqConstants::IsotopeMatrices 		IsotopeMatrices
 (user defined?) isotope correction matrix in (-2, -1, +1, +2) row style

Public Member Functions

 ItraqQuantifier ()
 Constructor (assuming 4-plex experiment).
 ItraqQuantifier (Int itraq_type)
 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.
 ItraqQuantifier (const ItraqQuantifier &cp)
 copy constructor
ItraqQuantifier & operator= (const ItraqQuantifier &rhs)
 assignment operator
void run (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out)
 using the raw iTRAQ intensities we apply isotope correction, normalization (using median)
ItraqQuantifierStats getStats () const

Protected Member Functions

void setDefaultParams_ ()
void updateMembers_ ()

Private Member Functions

void initIsotopeCorrections_ ()
 initialize
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.

Private Attributes

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

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

typedef ItraqConstants::ChannelInfo ChannelInfo
typedef ItraqConstants::ChannelMapType ChannelMapType

maps iTRAQ channel (e.g. 117) to more information

Reimplemented from ItraqConstants.

typedef ItraqConstants::IsotopeMatrices IsotopeMatrices

(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style

Reimplemented from ItraqConstants.

Constructor & Destructor Documentation

ItraqQuantifier (  ) 

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.

ItraqQuantifier ( const ItraqQuantifier &  cp  ) 

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:
The matrix 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_in Raw iTRAQ intensities from previous step
consensus_map_out Post-processed iTRAQ ratios for peptides
Exceptions:
Exception::FailedAPICall is least-squares fit fails
Exception::InvalidParameter if parameter is invalid (e.g. reference_channel)
void setDefaultParams_ (  )  [protected]
void updateMembers_ (  )  [protected]

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]

either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX

ItraqQuantifierStats stats_ [private]

stats for isotope correction

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1