Some constants used throughout iTRAQ classes. More...
#include <OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h>
Classes | |
| struct | ChannelInfo |
| stores information on an iTRAQ channel More... | |
Public Types | |
| 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 | |
| typedef std::vector< Matrix < double > > | IsotopeMatrices |
| (user defined?) isotope correction matrix in (-2, -1, +1, +2) row style | |
Static Public Member Functions | |
| static StringList | getIsotopeMatrixAsStringList (const int itraq_type, const IsotopeMatrices &isotope_corrections) |
| convert isotope correction matrix to stringlist | |
| static void | updateIsotopeMatrixFromStringList (const int itraq_type, const StringList &channels, IsotopeMatrices &isotope_corrections) |
| convert strings to isotope correction matrix rows | |
| static void | initChannelMap (const int itraq_type, ChannelMapType &map) |
| information about an iTRAQ channel | |
| static void | updateChannelMap (const StringList &active_channels, ChannelMapType &map) |
| activate & annotate channels | |
| 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 | |
Static Public Attributes | |
| static const Int | CHANNEL_COUNT [] |
| static const Int | CHANNELS_FOURPLEX [4][1] |
| channel names for 4plex( 114, 115, 116, 117) | |
| static const Int | CHANNELS_EIGHTPLEX [8][1] |
| channel names for 8plex( 113, 114, 115, 116, 117, 118, 119, 121) | |
| static const Int | CHANNELS_TMT_SIXPLEX [6][1] |
| channel names for 6plex TMT with CID fragmentation( 126, 127, 128, 129, 130, 131) | |
| static const double | ISOTOPECORRECTIONS_FOURPLEX [4][4] |
| default isotope correction matrix (4 plex) | |
| static const double | ISOTOPECORRECTIONS_EIGHTPLEX [8][4] |
| default isotope correction matrix (8 plex) | |
| static const double | ISOTOPECORRECTIONS_TMT_SIXPLEX [6][4] |
| default isotope correction matrix (6 plex TMT) | |
Detailed Description
Some constants used throughout iTRAQ classes.
Constants for iTRAQ experiments and a ChannelInfo structure to store information about a single channel.
Member Typedef Documentation
| typedef Map<Int, ChannelInfo> ChannelMapType |
maps iTRAQ channel (e.g. 117) to more information
Reimplemented in ItraqChannelExtractor, and ItraqQuantifier.
| typedef std::vector<Matrix<double> > IsotopeMatrices |
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Reimplemented in ItraqQuantifier.
Member Enumeration Documentation
| enum ITRAQ_TYPES |
Member Function Documentation
| static StringList getIsotopeMatrixAsStringList | ( | const int | itraq_type, | |
| const IsotopeMatrices & | isotope_corrections | |||
| ) | [static] |
convert isotope correction matrix to stringlist
Each line is converted into a string of the format <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' Useful for creating parameters or debug output.
- Parameters:
-
itraq_type Which matrix to stringify. Should be of values from enum ITRAQ_TYPES isotope_corrections Vector of the two matrices (4plex, 8plex).
| static void initChannelMap | ( | const int | itraq_type, | |
| ChannelMapType & | map | |||
| ) | [static] |
information about an iTRAQ channel
State, name and expected mz-position of iTRAQ channels are initialized.
- Parameters:
-
itraq_type Should be of values from enum ITRAQ_TYPES map Storage to initialize
| static Matrix<double> translateIsotopeMatrix | ( | const int & | itraq_type, | |
| const IsotopeMatrices & | isotope_corrections | |||
| ) | [static] |
translate isotope correction matrix in -2,-1,+1,+2 form into 114,115,116,117 format
Translates e.g. ItraqConstants::ISOTOPECORRECTIONS_EIGHTPLEX matrix into a 8x8 matrix which maps how channel (row) distributes its tags onto other channels (columns).
- Parameters:
-
itraq_type Should be of values from enum ITRAQ_TYPES isotope_corrections isotope correction matrix in -2...+2 form
| static void updateChannelMap | ( | const StringList & | active_channels, | |
| ChannelMapType & | map | |||
| ) | [static] |
activate & annotate channels
State and description of iTRAQ channels are updated. Each input string must have the format <channel>:<description>, e.g. "114:myref","115:liver"
- Parameters:
-
active_channels StringList with channel and description map Storage to update
| static void updateIsotopeMatrixFromStringList | ( | const int | itraq_type, | |
| const StringList & | channels, | |||
| IsotopeMatrices & | isotope_corrections | |||
| ) | [static] |
convert strings to isotope correction matrix rows
Each string of format <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' is parsed and the corresponding channel(row) in the matrix is updated. Not all channels need to be present, missing channels will be left untouched. Useful to update the matrix with user isotope correction values.
- Parameters:
-
itraq_type Which matrix to stringify. Should be of values from enum ITRAQ_TYPES channels New channel isotope values as strings isotope_corrections Vector of the two matrices (4plex, 8plex).
Member Data Documentation
const Int CHANNEL_COUNT[] [static] |
const Int CHANNELS_EIGHTPLEX[8][1] [static] |
channel names for 8plex( 113, 114, 115, 116, 117, 118, 119, 121)
const Int CHANNELS_FOURPLEX[4][1] [static] |
channel names for 4plex( 114, 115, 116, 117)
const Int CHANNELS_TMT_SIXPLEX[6][1] [static] |
channel names for 6plex TMT with CID fragmentation( 126, 127, 128, 129, 130, 131)
const double ISOTOPECORRECTIONS_EIGHTPLEX[8][4] [static] |
default isotope correction matrix (8 plex)
const double ISOTOPECORRECTIONS_FOURPLEX[4][4] [static] |
default isotope correction matrix (4 plex)
const double ISOTOPECORRECTIONS_TMT_SIXPLEX[6][4] [static] |
default isotope correction matrix (6 plex TMT)
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1 |