Metabolomics::Banks::MaConDa - Perl extension for contaminants bank building
Version 0.1
use Metabolomics::Banks::MaConDa;
Metabolomics::Banks::MaConDa is a full package for Perl allowing to build a generic Perl bank object from MaConDa resource.
## Description : new ## Input : $self ## Ouput : bless $self ; ## Usage : new() ;
## Description : set a new contaminant object ## Input : NA ## Output : $refContaminant ## Usage : my ( $refContaminant ) = __refContaminant__() ;
## Description : set a new contaminant object in extensive version ## Input : NA ## Output : $refContaminantExtensive ## Usage : my ( $refContaminantExtensive ) = __refContaminantExtensive__() ;
## Description : get all contaminants information from the MaConDa resources v01 ## Input : $source ## Output : $oBank ## Usage : my ( $oBank ) = getContaminantsFromSource ( $source ) ;
## Description : get all contaminants information from the MaConDa extensive resources v01 ## Input : $source ## Output : $oBank ## Usage : my ( $oBank ) = getContaminantsFromSource ( $source ) ;
## Description : building a bank integrating each potential ion from contaminants ## Input : $refBank, $oContaminants, $queryMode ## Output : $ionBank ## Usage : my ( $ionBank ) = buildTheoPeakBankFromContaminants ( $refBank, $oContaminants, $queryMode ) ;
## Description : extract contaminant types listing from contaminants object ## Input : $oContaminants ## Output : $contaminantTypes ## Usage : my ( $contaminantTypes ) = extractContaminantTypes ( $oContaminants ) ;
## Description : extract instruments listing from contaminants object ## Input : $oContaminants ## Output : $contaminantInstruments ## Usage : my ( $contaminantInstruments ) = extractContaminantInstruments ( $oContaminants ) ;
## Description : extract instrument types listing from contaminants object ## Input : $oContaminants ## Output : $contaminantInstrumentTypes ## Usage : my ( $contaminantInstrumentTypes ) = extractContaminantInstrumentTypes ( $oContaminants ) ;
## Description : filtering contaminants by their ion mode (POS|NEG|BOTH) ## Input : $oBank, $ionMode ## Output : $oFilteredBank ## Usage : my ( $oFilteredBank ) = filterContaminantIonMode ( $oBank, $ionMode ) ;
## Description : filtering contaminants by their instrument (array) ## Input : $oBank, $instruments ## Output : $oFilteredBank, $totalEntryNum, $fiteredEntryNum ## Usage : my ( $oFilteredBank ) = filterContaminantInstruments ( $oBank, $instruments ) ;
## Description : filtering contaminants by their instrument types (array) ## Input : $oBank, $instrumentTypes ## Output : $oFilteredBank ## Usage : my ( $oFilteredBank ) = filterContaminantInstrumentTypes ( $oBank, $instrumentTypes ) ;
## Description : _setContaminantExtREFERENCE ## Input : $REFERENCE ## Output : TRUE ## Usage : _setContaminantExtREFERENCE ( $ION_FORM ) ;
## Description : _getContaminantExtION_MODE ## Input : void ## Output : $ION_MODE ## Usage : my ( $ION_MODE ) = _getContaminantExtION_MODE () ;
## Description : _setContaminantExtION_MODE ## Input : $ION_MODE ## Output : TRUE ## Usage : _setContaminantExtION_MODE ( $ION_FORM ) ;
## Description : _setContaminantExtEXACT_ADDUCT_MASS ## Input : $EXACT_ADDUCT_MASS ## Output : TRUE ## Usage : _setContaminantExtEXACT_ADDUCT_MASS ( $ION_FORM ) ;
## Description : _getContaminantExtEXACT_ADDUCT_MASS ## Input : void ## Output : $EXACT_ADDUCT_MASS ## Usage : my ( $EXACT_ADDUCT_MASS ) = _getContaminantExtEXACT_ADDUCT_MASS () ;
## Description : _getContaminantExtION_FORM ## Input : void ## Output : $ION_FORM ## Usage : my ( $ION_FORM ) = _getContaminantExtION_FORM () ;
## Description : _setContaminantExtION_FORM ## Input : $ION_FORM ## Output : TRUE ## Usage : _setContaminantExtION_FORM ( $ION_FORM ) ;
## Description : _getContaminantExtMZ ## Input : void ## Output : $MZ ## Usage : my ( $EXACT_ADDUCT_MASS ) = _getContaminantExtMZ () ;
## Description : _setContaminantExtMZ ## Input : $MZ ## Output : TRUE ## Usage : _setContaminantExtMZ ( $MZ ) ;
## Description : _getContaminantExtINSTRUMENT_TYPES ## Input : void ## Output : $INSTRUMENT_TYPE ## Usage : my ( $INSTRUMENT_TYPE ) = _getContaminantExtINSTRUMENT_TYPES () ;
## Description : _setContaminantExtINSTRUMENT_TYPE ## Input : $INSTRUMENT_TYPE ## Output : TRUE ## Usage : _setContaminantExtINSTRUMENT_TYPE ( $INSTRUMENT_TYPE ) ;
## Description : _getContaminantExtINSTRUMENTS ## Input : void ## Output : $INSTRUMENT ## Usage : my ( $INSTRUMENT ) = _getContaminantExtINSTRUMENTS () ;
## Description : _setContaminantExtINSTRUMENT ## Input : $INSTRUMENT ## Output : TRUE ## Usage : _setContaminantExtINSTRUMENT ( $INSTRUMENT ) ;
## Description : _setContaminantExtCHROMATOGRAPHY ## Input : $CHROMATOGRAPHY ## Output : TRUE ## Usage : _setContaminantExtCHROMATOGRAPHY ( $CHROMATOGRAPHY ) ;
## Description : _setContaminantExtION_SOURCE_TYPE ## Input : $ION_SOURCE_TYPE ## Output : TRUE ## Usage : _setContaminantExtION_SOURCE_TYPE ( $ION_SOURCE_TYPE ) ;
## Description : _getContaminantExtTYPE_OF_CONTAMINANT ## Input : void ## Output : $TYPE_OF_CONTAMINANT ## Usage : my ( $TYPE_OF_CONTAMINANT ) = _getContaminantExtTYPE_OF_CONTAMINANT () ;
## Description : _setContaminantTYPE_OF_CONTAMINANT ## Input : $TYPE_OF_CONTAMINANT ## Output : TRUE ## Usage : _setContaminantTYPE_OF_CONTAMINANT ( $TYPE_OF_CONTAMINANT ) ;
## Description : _setContaminantPUBCHEM_CID ## Input : $PUBCHEM_CID ## Output : TRUE ## Usage : _setContaminantPUBCHEM_CID ( $PUBCHEM_CID ) ;
## Description : _setContaminantSTD_INCHI_KEY ## Input : $STD_INCHI_KEY ## Output : TRUE ## Usage : _setContaminantSTD_INCHI_KEY ( $STD_INCHI_KEY ) ;
## Description : _setContaminantSTD_INCHI ## Input : $STD_INCHI ## Output : TRUE ## Usage : _setContaminantSTD_INCHI ( $STD_INCHI ) ;
## Description : _getContaminantEXACT_MASS ## Input : void ## Output : $EXACT_MASS ## Usage : my ( $EXACT_MASS ) = _getContaminantEXACT_MASS () ;
## Description : _setContaminantEXACT_MASS ## Input : $EXACT_MASS ## Output : TRUE ## Usage : _setContaminantEXACT_MASS ( $EXACT_MASS ) ;
## Description : _setContaminantFORMULA ## Input : $FORMULA ## Output : TRUE ## Usage : _setContaminantFORMULA ( $FORMULA ) ;
## Description : _getContaminantNAME ## Input : void ## Output : $NAME ## Usage : my ( $NAME ) = _getContaminantNAME () ;
## Description : _setContaminantNAME ## Input : $NAME ## Output : TRUE ## Usage : _setContaminantNAME ( $NAME ) ;
## Description : _getContaminantID ## Input : void ## Output : $ID ## Usage : my ( $ID ) = _getContaminantID () ;
## Description : _setContaminantID ## Input : $ID ## Output : TRUE ## Usage : _setContaminantID ( $ID ) ;
Franck Giacomoni, <franck.giacomoni at inra.fr>
<franck.giacomoni at inra.fr>
All information about Metabolomics::Fragment would be find here: https://services.pfem.clermont.inra.fr/gitlab/fgiacomoni/metabolomics-fragnot
Please report any bugs or feature requests to bug-Metabolomics-Fragment-Annotation at rt.cpan.org, or through the web interface at https://rt.cpan.org/Public/Dist/Display.html?Name=Metabolomics-Fragment-Annotation. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
bug-Metabolomics-Fragment-Annotation at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Metabolomics::Banks::MaConDa
RT: CPAN's request tracker (report bugs here)
https://rt.cpan.org/Public/Dist/Display.html?Name=Metabolomics-Fragment-Annotation
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Metabolomics-Fragment-Annotation
CPAN Ratings
https://cpanratings.perl.org/d/Metabolomics-Fragment-Annotation
Search CPAN
https://metacpan.org/release/Metabolomics-Fragment-Annotation
CeCILL Copyright (C) 2019 by Franck Giacomoni
Initiated by Franck Giacomoni
followed by INRA PFEM team
Web Site = INRA PFEM
To install Metabolomics::Fragment::Annotation, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Metabolomics::Fragment::Annotation
CPAN shell
perl -MCPAN -e shell install Metabolomics::Fragment::Annotation
For more information on module installation, please visit the detailed CPAN module installation guide.