Metabolomics::Banks - Perl extension to build metabolite banks for metabolomics
Version 0.01
use Metabolomics::Fragment::Annotation;
Metabolomics::Fragment::Annotation is a full package for Perl dev allowing full annotation of fragments.
## Description : set a new bank object ## Input : NA ## Output : $oBank ## Usage : my ( $oBank ) = Metabolomics::Banks->new ( ) ;
## Description : set_DATABASE_ENTRIES_NB ## Input : $DATABASE_ENTRIES_NB ## Output : TRUE ## Usage : $self->set_DATABASE_ENTRIES_NB ( $DATABASE_ENTRIES_NB ) ;
## Description : _addEntry ## Input : $self, $Entry ; ## Ouput : NA ## Usage : _addEntry($Entry);
## Description : _addFragment ## Input : $self, $fragment ; ## Ouput : NA ## Usage : _addFragment($fragment);
## Description : _addContaminant ## Input : $self, $contaminant ; ## Ouput : NA ## Usage : _addContaminant($contaminant);
## Description : get the list of contaminants from the bank object ## Input : $self ## Output : $contaminants ## Usage : my ( $contaminants ) = $obank->_getContaminants () ;
## Description : get the list of entries from the bank object ## Input : $self ## Output : $Entries ## Usage : my ( $Entries ) = $obank->_getEntries () ;
## Description : get the list of fragments from the bank object ## Input : $self ## Output : $fragments ## Usage : my ( $fragments ) = $obank->_getFragments () ;
## Description : set a new theorical peak ## Input : NA ## Output : refPeak ## Usage : my ( refPeak ) = __refPeak__() ;
## Description : _addPeakList ## Input : $self, $type, $peakList ; ## Ouput : NA; ## Usage : _addPeakList($type, $peakList);
## Description : get the list of fragments from the bank object ## Input : $self, $type ## Output : $peakList ## Usage : my ( $peakList ) = $obank->_getPeakList ($type) ;
## Description : _setPeak_COMPUTED_MONOISOTOPIC_MASS ## Input : $COMPUTED_MONOISOTOPIC_MASS ## Output : TRUE ## Usage : _setPeak_COMPUTED_MONOISOTOPIC_MASS ( $COMPUTED_MONOISOTOPIC_MASS ) ;
## Description : _getPeakCOMPUTED_MONOISOTOPIC_MASS ## Input : void ## Output : $COMPUTED_MONOISOTOPIC_MASS ## Usage : my ( $COMPUTED_MONOISOTOPIC_MASS ) = _getPeakCOMPUTED_MONOISOTOPIC_MASS () ;
## Description : _setPeakMESURED_MONOISOTOPIC_MASS ## Input : $MESURED_MONOISOTOPIC_MASS ## Output : TRUE ## Usage : _setPeakMESURED_MONOISOTOPIC_MASS ( $MESURED_MONOISOTOPIC_MASS ) ;
## Description : _getPeakMESURED_MONOISOTOPIC_MASS ## Input : void ## Output : $MESURED_MONOISOTOPIC_MASS ## Usage : my ( $MESURED_MONOISOTOPIC_MASS ) = _getPeakMESURED_MONOISOTOPIC_MASS () ;
## Description : _setANNOTATION_IN_NEG_MODE ## Input : $ANNOTATION_IN_NEG_MODE ## Output : TRUE ## Usage : _setANNOTATION_IN_NEG_MODE ( $ANNOTATION_IN_NEG_MODE ) ;
## Description : _getPeak_ANNOTATION_IN_NEG_MODE ## Input : void ## Output : $ANNOTATION_IN_NEG_MODE ## Usage : my ( $ANNOTATION_IN_NEG_MODE ) = _getPeak_ANNOTATION_IN_NEG_MODE () ;
## Description : _setANNOTATION_DA_ERROR ## Input : $MMU_ERROR ## Output : TRUE ## Usage : _setANNOTATION_DA_ERROR ( $MMU_ERROR ) ;
## Description : _setANNOTATION_PPM_ERROR ## Input : $PPM_ERROR ## Output : TRUE ## Usage : _setANNOTATION_PPM_ERROR ( $PPM_ERROR ) ;
## Description : _setANNOTATION_IN_NEG_MODE ## Input : $ANNOTATION_IN_POS_MODE ## Output : TRUE ## Usage : _setANNOTATION_IN_POS_MODE ( $ANNOTATION_IN_POS_MODE ) ;
## Description : _getPeak_ANNOTATION_IN_POS_MODE ## Input : void ## Output : $ANNOTATION_IN_POS_MODE ## Usage : my ( $ANNOTATION_IN_POS_MODE ) = _getPeak_ANNOTATION_IN_POS_MODE () ;
## Description : _setPeak_ANNOTATION_TYPE ## Input : $ANNOTATION_TYPE ## Output : TRUE ## Usage : _setPeak_ANNOTATION_TYPE ( $ANNOTATION_TYPE ) ;
## Description : _getPeak_ANNOTATION_TYPE ## Input : void ## Output : $ANNOTATION_TYPE ## Usage : my ( $TYPE ) = _getPeak_ANNOTATION_TYPE () ;
## Description : _setANNOTATION_NAME ## Input : $ANNOTATION_NAME ## Output : TRUE ## Usage : _setANNOTATION_NAME ( $ANNOTATION_NAME ) ;
## Description : _getPeak_ANNOTATION_NAME ## Input : void ## Output : $ANNOTATION_NAME ## Usage : my ( $ANNOTATION_NAME ) = _getPeak_ANNOTATION_NAME () ;
## Description : _getPeak_ANNOTATION_ID ## Input : void ## Output : $ANNOTATION_ID ## Usage : my ( $ANNOTATION_ID ) = _getPeak_ANNOTATION_ID () ;
## Description : _setANNOTATION_ID ## Input : $ANNOTATION_ID ## Output : TRUE ## Usage : _setANNOTATION_ID ( $ANNOTATION_ID ) ;
## Description : _setPeak_ANNOTATION_ONLY_IN ## Input : $ANNOTATION_ONLY_IN ## Output : TRUE ## Usage : _setPeak_ANNOTATION_ONLY_IN ( $ANNOTATION_ONLY_IN ) ;
## Description : get a list of Ms fragment from a experimental mesureament. ## Input : $oBank, $Xfile, $is_header, $column ## Output : $msFragBank ## Usage : $oBank->parsingMsFragments ( $Xfile, $is_header, $column ) ;
## Description : compute the mz of a neutral cpd into the positive ion form mz ## Input : $initMz, $charge ## Output : $positiveMz ## Usage : my ( $positiveMz ) = computeNeutralCpdMz_To_PositiveIonMz ( $initMz, $charge ) ;
## Description : compute the mz of a neutral cpd into the positive ion form mz ## Input : $initMz, $chargeNumber ## Output : $negativeMz ## Usage : my ( $negativeMz ) = computeNeutralCpdMz_To_NegativeIonMz ( $initMz, $chargeNumber ) ;
Franck Giacomoni, <franck.giacomoni at inra.fr>
<franck.giacomoni at inra.fr>
All information about Metabolomics::Banks 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
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.