Does post-processing on raw iTRAQ channel quantitation. More...
#include <OpenMS/ANALYSIS/QUANTITATION/ItraqQuantifier.h>
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 |
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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 | |
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 ¶m) | |
Constructor with iTRAQ-type (either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX) and Param. More... | |
ItraqQuantifier (const ItraqQuantifier &cp) | |
copy constructor More... | |
ItraqQuantifier & | operator= (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 |
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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_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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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 | |
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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... | |
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:Name | Type | Default | Restrictions | Description |
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isotope_correction | string | true | true, false | Enable isotope correction (highly recommended). |
do_normalization | string | false | true, false | Normalize 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 | int | 114 | min: 114 max: 117 | Number 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: |
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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: |
ItraqQuantifier | ( | ) |
Constructor (assuming 4-plex experiment)
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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
ItraqQuantifierStats getStats | ( | ) | const |
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private |
initialize
Check if the given channel_frequency matrix is an identity matrix.
The | matrix to check. |
ItraqQuantifier& operator= | ( | const ItraqQuantifier & | rhs | ) |
assignment operator
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private |
void run | ( | const ConsensusMap & | consensus_map_in, |
ConsensusMap & | consensus_map_out | ||
) |
using the raw iTRAQ intensities we apply isotope correction, normalization (using median)
consensus_map_in | Raw iTRAQ intensities from previous step |
consensus_map_out | Post-processed iTRAQ ratios for peptides |
Exception::FailedAPICall | is least-squares fit fails |
Exception::InvalidParameter | if parameter is invalid (e.g. reference_channel) |
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protected |
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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.
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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
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private |
Matrices with isotope correction values (one for each plex-type)
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private |
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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 |