Metabolomics::Banks::AbInitioFragments(3)

NAME
Metabolomics::Banks::AbInitioFragments - Perl extension for Ab Initio Fragments generator

VERSION
Version 0.3 - Adding POD

SYNOPSIS
use Metabolomics::Banks::AbInitioFragments;

DESCRIPTION
Metabolomics::Banks::AbInitioFragments is a full package for Perl allowing to build a generic Perl bank object from Ab Initio fragments resource.

EXPORT
use Metabolomics::Banks::AbInitioFragments qw( :all ) ;

PUBLIC METHODS

  Metabolomics::Banks::AbInitioFragments

new
            ## Description : new
            ## Input : $self
            ## Ouput : bless $self ;
            ## Usage : new() ;

METHOD getFragmentsFromSource
            ## Description : get the list of theorical fragments from $source file
            ## Input : $source
            ## Output : $theoFragments
            ## Usage : my ( $theoFragments ) = getFragmentsFromSource ( $source ) ;

METHOD buildTheoPeakBankFromFragments
            ## Description : building a bank integrating each potential fragments from a parent ion
            ## Input : $refBank, $mzParent, $mode (POSITIVE, NEGATIVE, NEUTRAL), $stateMolecule (POS, NEG, NEU)
            ## Output : $ionBank
            ## Usage : my ( $ionBank ) = buildTheoPeakBankFromFragments ( $refBank, $mzParent ) ;

METHOD buildTheoDimerFromMz
            ## Description : build potential dimers/trimers in NEG/POS mode
            ## Input : $Mz, $mode
            ## Output : $oBank
            ## Usage : my ( $oBank ) = buildTheoDimerFromMz ( $Mz, $mode ) ;

METHOD isotopicAdvancedCalculation
            ## Description : if a fragment is present in theorical bank, compute its isotopic couple.
            ## Input : $refBank
            ## Output : $ionBank
            ## Usage : my ( $ionBank ) = isotopicAdvancedCalculation ( $refBank ) ;

PRIVATE METHODS

  Metabolomics::Banks::AbInitioFragments

PRIVATE_ONLY __refBloodExposomeEntry__
            ## Description : init a new ab initio fragment entry
            ## Input : void
            ## Output : refEntry
            ## Usage : $self->__refAbInitioFragment__() ;

PRIVATE_ONLY _getANNOTATION_IN_NEG_MODE
            ## Description : _getANNOTATION_IN_NEG_MODE
            ## Input : void
            ## Output : $ANNOTATION_IN_NEG_MODE
            ## Usage : my ( $ANNOTATION_IN_NEG_MODE ) = _getANNOTATION_IN_NEG_MODE () ;

PRIVATE_ONLY _getANNOTATION_IN_POS_MODE
            ## Description : _getANNOTATION_IN_POS_MODE
            ## Input : void
            ## Output : $ANNOTATION_IN_POS_MODE
            ## Usage : my ( $ANNOTATION_IN_POS_MODE ) = _getANNOTATION_IN_POS_MODE () ;

PRIVATE_ONLY _getDELTA_MASS
            ## Description : _getDELTA_MASS
            ## Input : void
            ## Output : $DELTA_MASS
            ## Usage : my ( $DELTA_MASS ) = _getDELTA_MASS () ;

PRIVATE_ONLY _getFragment_TYPE
            ## Description : _getFragment_TYPE
            ## Input : void
            ## Output : $TYPE
            ## Usage : my ( $TYPE ) = _getFragment_TYPE () ;

PRIVATE_ONLY _getLOSSES_OR_GAINS
            ## Description : _getLOSSES_OR_GAINS
            ## Input : void
            ## Output : $LOSSES_OR_GAINS
            ## Usage : my ( $LOSSES_OR_GAINS ) = _getLOSSES_OR_GAINS () ;

AUTHOR
Franck Giacomoni, "<franck.giacomoni at inrae.fr>"

SEE ALSO
All information about Metabolomics::Fragment::Annotation would be find here: https://services.pfem.clermont.inra.fr/gitlab/fgiacomoni/metabolomics-fragnot

BUGS
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.

SUPPORT
You can find documentation for this module with the perldoc command.

    perldoc Metabolomics::Banks::AbInitioFragments

•   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>

ACKNOWLEDGEMENTS
Thank you to INRAE and All metabolomics colleagues.

LICENSE AND COPYRIGHT
CeCILL Copyright (C) 2019 by Franck Giacomoni

Initiated by Franck Giacomoni

followed by INRAE PFEM team

Web Site = INRAE PFEM