NAME

Metabolomics::Banks - Perl extension to build metabolite banks for metabolomics

VERSION

Version 0.3 - Object integration for multi-annotation Version 0.4 - Completing object properties and add cluster support Version 0.5 - parsingFeaturesFragments method to manage complexe fragments (multiple features)

SYNOPSIS

use Metabolomics::Banks

DESCRIPTION

Metabolomics::Banks is a meta class for bank objects.

EXPORT

use Metabolomics::Banks qw( :all ) ;

PUBLIC METHODS

Metabolomics::Fragment::Annotation

new

## Description : set a new bank object
## Input : NA
## Output : $oBank
## Usage : my ( $oBank ) = Metabolomics::Banks->new ( ) ;

computeNeutralCpdMz_To_PositiveIonMz

## 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 ) ;

computeNeutralCpdMz_To_NegativeIonMz

## 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 ) ;

getMinAndMaxMass

## Description : retrieve the min/max mz of a __PEAK_LIST_
## Input : N/A
## Output : $minMs, $maxMs
## Usage : my ( $minMs, $maxMs ) = getMinAndMaxMass() ;

parsingMsFragments

## 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 ) ;

parsingMsFragmentsByCluster

## 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 ) ;

parsingFeaturesFragments

## Description : get a list of fragments from a experimental mesureament with all their features.
## Input : $oBank, $Xfile, $is_header, $columns
## Output : $msFragBank
## Usage : $oBank->parsingFeaturesFragments ( $Xfile, $is_header, $columns ) ;

PRIVATE METHODS

Metabolomics::Banks

PRIVATE_ONLY _set_DATABASE_ENTRIES_NB

## Description : _set_DATABASE_ENTRIES_NB
## Input : $DATABASE_ENTRIES_NB
## Output : TRUE
## Usage : $self->_set_DATABASE_ENTRIES_NB ( $DATABASE_ENTRIES_NB ) ;

PRIVATE_ONLY _addEntry

## Description : _addEntry
## Input : $self, $Entry ;
## Ouput :  NA
## Usage : _addEntry($Entry);

PRIVATE_ONLY _addSpectra

## Description : _addSpectra
## Input : $self, $Entry, $Index ;
## Ouput :  NA
## Usage : _addSpectra($Entry, $Index);

PRIVATE_ONLY _indexSpectraByCluster

## Description : _indexSpectraByCluster
## Input : $self, $clusterID, $spectralID ;
## Ouput :  NA
## Usage : $self->_indexSpectraByCluster($clusterID, $spectralID);

PRIVATE_ONLY _detectSpectraDuplicate

## Description : _detectSpectraDuplicate
## Input : $self, $spectralID ;
## Ouput :  TRUE/FALSE
## Usage : $self->_detectSpectraDuplicate($spectralID);

PRIVATE_ONLY _addFragment

## Description : _addFragment
## Input : $self, $fragment ;
## Ouput :  NA
## Usage : _addFragment($fragment);

PRIVATE_ONLY _addContaminant

## Description : _addContaminant
## Input : $self, $contaminant ;
## Ouput :  NA
## Usage : _addContaminant($contaminant);

PRIVATE_ONLY _getContaminants

## Description : get the list of contaminants from the bank object
## Input : $self
## Output : $contaminants
## Usage : my ( $contaminants ) = $obank->_getContaminants () ;

PRIVATE_ONLY _getEntries

## Description : get the list of entries from the bank object
## Input : $self
## Output : $Entries
## Usage : my ( $Entries ) = $obank->_getEntries () ;

PRIVATE_ONLY _getSpectra

## Description : get the list of entries from the bank object
## Input : $self
## Output : $Entries
## Usage : my ( $Entries ) = $obank->_getSpectra () ;

PRIVATE_ONLY _getFragments

## Description : get the list of fragments from the bank object
## Input : $self
## Output : $fragments
## Usage : my ( $fragments ) = $obank->_getFragments () ;

PRIVATE_ONLY _getTheoricalPeaks

## Description : get the list of theorical peaks from the bank object
## Input : $self
## Output : $theoPeaks
## Usage : my ( $theoPeaks ) = $obank->_getTheoricalPeaks () ;

PRIVATE_ONLY __refPeak__

## Description : set a new theorical peak
## Input : NA	
## Output : refPeak
## Usage : my ( refPeak ) = __refPeak__() ;

PRIVATE_ONLY _addPeakList

## Description : _addPeakList
## Input : $self, $type, $peakList ;
## Ouput : NA;
## Usage : _addPeakList($type, $peakList);

PRIVATE_ONLY _getPeakList

## Description : get the list of fragments from the bank object
## Input : $self, $type
## Output : $peakList
## Usage : my ( $peakList ) = $obank->_getPeakList ($type) ;

PRIVATE_ONLY _setPeak_COMPUTED_MONOISOTOPIC_MASS

## Description : _setPeak_COMPUTED_MONOISOTOPIC_MASS
## Input : $COMPUTED_MONOISOTOPIC_MASS
## Output : TRUE
## Usage : _setPeak_COMPUTED_MONOISOTOPIC_MASS ( $COMPUTED_MONOISOTOPIC_MASS ) ;

PRIVATE_ONLY _getPeakCOMPUTED_MONOISOTOPIC_MASS

## Description : _getPeakCOMPUTED_MONOISOTOPIC_MASS
## Input : void
## Output : $COMPUTED_MONOISOTOPIC_MASS
## Usage : my ( $COMPUTED_MONOISOTOPIC_MASS ) = _getPeakCOMPUTED_MONOISOTOPIC_MASS () ;

PRIVATE_ONLY _setPeakMESURED_MONOISOTOPIC_MASS

## Description : _setPeakMESURED_MONOISOTOPIC_MASS
## Input : $MESURED_MONOISOTOPIC_MASS
## Output : TRUE
## Usage : _setPeakMESURED_MONOISOTOPIC_MASS ( $MESURED_MONOISOTOPIC_MASS ) ;

PRIVATE_ONLY _getPeakMESURED_MONOISOTOPIC_MASS

## Description : _getPeakMESURED_MONOISOTOPIC_MASS
## Input : void
## Output : $MESURED_MONOISOTOPIC_MASS
## Usage : my ( $MESURED_MONOISOTOPIC_MASS ) = _getPeakMESURED_MONOISOTOPIC_MASS () ;

PRIVATE_ONLY _setPeak_CLUSTER_ID

## Description : _setPeak_CLUSTER_ID
## Input : $VALUE
## Output : TRUE
## Usage : _setPeak_CLUSTER_ID ( $VALUE ) ;

PRIVATE_ONLY _getPeak_CLUSTER_ID

## Description : _getPeak_CLUSTER_ID
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeak_CLUSTER_ID () ;

PRIVATE_ONLY _setPeakFilterPass

## Description : _setPeakFilterPass
## Input : $VALUE
## Output : TRUE
## Usage : _setPeakFilterPass ( $VALUE ) ;

PRIVATE_ONLY _getPeakFilterPass

## Description : _getPeakFilterPass
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeakFilterPass () ;

PRIVATE_ONLY _setPeak_RELATIVE_INTENSITY_100

## Description : _setPeak_RELATIVE_INTENSITY_100
## Input : $VALUE
## Output : TRUE
## Usage : _setPeak_RELATIVE_INTENSITY_100 ( $VALUE ) ;

PRIVATE_ONLY _getPeak_RELATIVE_INTENSITY_100

## Description : _getPeak_RELATIVE_INTENSITY_100
## Input : void
## Output : $MESURED_MONOISOTOPIC_MASS
## Usage : my ( $MESURED_MONOISOTOPIC_MASS ) = _getPeak_RELATIVE_INTENSITY_100 () ;

PRIVATE_ONLY _setPeak_RELATIVE_INTENSITY_999

## Description : _setPeak_RELATIVE_INTENSITY_999
## Input : $VALUE
## Output : TRUE
## Usage : _setPeak_RELATIVE_INTENSITY_999 ( $VALUE ) ;

PRIVATE_ONLY _getPeak_RELATIVE_INTENSITY_999

## Description : _getPeak_RELATIVE_INTENSITY_999
## Input : void
## Output : $MESURED_MONOISOTOPIC_MASS
## Usage : my ( $MESURED_MONOISOTOPIC_MASS ) = _getPeak_RELATIVE_INTENSITY_999 () ;

PRIVATE_ONLY _setPeak_INTENSITY

## Description : _setPeak_INTENSITY
## Input : $INTENSITY
## Output : TRUE
## Usage : _setPeak_INTENSITY ( $INTENSITY ) ;

PRIVATE_ONLY _getPeak_INTENSITY

## Description : _getPeak_INTENSITY
## Input : void
## Output : $MESURED_MONOISOTOPIC_MASS
## Usage : my ( $MESURED_MONOISOTOPIC_MASS ) = _getPeak_INTENSITY () ;

PRIVATE_ONLY _setANNOTATION_IN_NEG_MODE

## Description : _setANNOTATION_IN_NEG_MODE
## Input : $ANNOTATION_IN_NEG_MODE
## Output : TRUE
## Usage : _setANNOTATION_IN_NEG_MODE ( $ANNOTATION_IN_NEG_MODE ) ;

PRIVATE_ONLY _getPeak_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 () ;

PRIVATE_ONLY _setANNOTATION_DA_ERROR

## Description : _setANNOTATION_DA_ERROR
## Input : $MMU_ERROR
## Output : TRUE
## Usage : _setANNOTATION_DA_ERROR ( $MMU_ERROR ) ;

PRIVATE_ONLY _setANNOTATION_PPM_ERROR

## Description : _setANNOTATION_PPM_ERROR
## Input : $PPM_ERROR
## Output : TRUE
## Usage : _setANNOTATION_PPM_ERROR ( $PPM_ERROR ) ;

PRIVATE_ONLY _setANNOTATION_IN_NEG_MODE

## Description : _setANNOTATION_IN_NEG_MODE
## Input : $ANNOTATION_IN_POS_MODE
## Output : TRUE
## Usage : _setANNOTATION_IN_POS_MODE ( $ANNOTATION_IN_POS_MODE ) ;

PRIVATE_ONLY _getPeak_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 () ;

PRIVATE_ONLY _setPeak_ANNOTATION_TYPE

## Description : _setPeak_ANNOTATION_TYPE
## Input : $ANNOTATION_TYPE
## Output : TRUE
## Usage : _setPeak_ANNOTATION_TYPE ( $ANNOTATION_TYPE ) ;

PRIVATE_ONLY _setPeak_ANNOTATIONS

## Description : _setPeak_ANNOTATIONS
## Input : $ANNOTATIONS
## Output : TRUE
## Usage : _setPeak_ANNOTATIONS ( $ANNOTATIONS ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_TYPE

## Description : _getPeak_ANNOTATION_TYPE
## Input : void
## Output : $ANNOTATION_TYPE
## Usage : my ( $TYPE ) = _getPeak_ANNOTATION_TYPE () ;

PRIVATE_ONLY _setANNOTATION_NAME

## Description : _setANNOTATION_NAME
## Input : $ANNOTATION_NAME
## Output : TRUE
## Usage : _setANNOTATION_NAME ( $ANNOTATION_NAME ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_NAME

## Description : _getPeak_ANNOTATION_NAME
## Input : void
## Output : $ANNOTATION_NAME
## Usage : my ( $ANNOTATION_NAME ) = _getPeak_ANNOTATION_NAME () ;

PRIVATE_ONLY _getPeak_ANNOTATION_ID

## Description : _getPeak_ANNOTATION_ID
## Input : void
## Output : $ANNOTATION_ID
## Usage : my ( $ANNOTATION_ID ) = _getPeak_ANNOTATION_ID () ;

PRIVATE_ONLY _getPeak_ANNOTATION_DA_ERROR

## Description : _getPeak_ANNOTATION_DA_ERROR
## Input : void
## Output : $ANNOTATION_DA_ERROR
## Usage : my ( $ANNOTATION_DA_ERROR ) = _getPeak_ANNOTATION_DA_ERROR () ;

PRIVATE_ONLY _getPeak_ANNOTATION_PPM_ERROR

## Description : _getPeak_ANNOTATION_PPM_ERROR
## Input : void
## Output : $ANNOTATION_ID
## Usage : my ( $ANNOTATION_ID ) = _getPeak_ANNOTATION_PPM_ERROR () ;

PRIVATE_ONLY _getPeak_ANNOTATION_SPECTRA_ID

## Description : _getPeak_ANNOTATION_SPECTRA_ID
## Input : void
## Output : $ANNOTATION_ID
## Usage : my ( $ANNOTATION_ID ) = _getPeak_ANNOTATION_SPECTRA_ID () ;

PRIVATE_ONLY _setPeak_ANNOTATION_ID

## Description : _setPeak_ANNOTATION_ID
## Input : $ANNOTATION_ID
## Output : TRUE
## Usage : _setPeak_ANNOTATION_ID ( $ANNOTATION_ID ) ;

PRIVATE_ONLY _setPeak_ANNOTATION_SPECTRA_ID

## Description : _setPeak_ANNOTATION_SPECTRA_ID
## Input : $ANNOTATION_ID
## Output : TRUE
## Usage : _setPeak_ANNOTATION_SPECTRA_ID ( $ANNOTATION_ID ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_FORMULA

## Description : _getPeak_ANNOTATION_FORMULA
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_FORMULA () ;

PRIVATE_ONLY _setPeak_ANNOTATION_FORMULA

## Description : _setPeak_ANNOTATION_FORMULA
## Input : $ANNOTATION_FORMULA
## Output : TRUE
## Usage : $self->_setPeak_ANNOTATION_FORMULA ( $ANNOTATION_ID ) ;

PRIVATE_ONLY _setPeak_ANNOTATION_ONLY_IN

## Description : _setPeak_ANNOTATION_ONLY_IN
## Input : $ANNOTATION_ONLY_IN
## Output : TRUE
## Usage : _setPeak_ANNOTATION_ONLY_IN ( $ANNOTATION_ONLY_IN ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_SMILES

## Description : _getPeak_ANNOTATION_SMILES
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_SMILES () ;

PRIVATE_ONLY _setPeak_ANNOTATION_SMILES

## Description : _setPeak_ANNOTATION_SMILES
## Input : $VALUE
## Output : TRUE
## Usage : _setPeak_ANNOTATION_SMILES ( $VALUE ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_INCHIKEY

## Description : _getPeak_ANNOTATION_INCHIKEY
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_INCHIKEY () ;

PRIVATE_ONLY _getPeak_ANNOTATIONS

## Description : _getPeak_ANNOTATIONS
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeak_ANNOTATIONS () ;

PRIVATE_ONLY _getPeak_ANNOTATION_SPECTRAL_IDS

## Description : _getPeak_ANNOTATION_SPECTRAL_IDS
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_SPECTRAL_IDS () ;

PRIVATE_ONLY _setPeak_ANNOTATION_SPECTRAL_IDS

## Description : _setPeak_ANNOTATION_SPECTRAL_IDS
## Input : $VALUE
## Output : TRUE
## Usage : _setPeak_ANNOTATION_SPECTRAL_IDS ( $VALUE ) ;

PRIVATE_ONLY _setPeak_ANNOTATION_INCHIKEY

## Description : _setPeak_ANNOTATION_INCHIKEY
## Input : $VALUE
## Output : TRUE
## Usage : _setPeak_ANNOTATION_INCHIKEY ( $VALUE ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_IS_A_PRECURSOR

## Description : _getPeak_ANNOTATION_IS_A_PRECURSOR
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_IS_A_PRECURSOR () ;

PRIVATE_ONLY _setPeak_ANNOTATION_IS_A_PRECURSOR

## Description : _setPeak_ANNOTATION_IS_A_PRECURSOR
## Input : $VALUE
## Output : TRUE
## Usage : _setPeak_ANNOTATION_IS_A_PRECURSOR ( $VALUE ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_IS_A_PRECURSOR

## Description : _getPeak_ANNOTATION_IS_A_PRECURSOR
## Input : void
## Output : $VALUE
## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_IS_A_PRECURSOR () ;

PRIVATE_ONLY _setPeak_ANNOTATION_IS_A_METABOLITE

## Description : _setPeak_ANNOTATION_IS_A_METABOLITE
## Input : $VALUE
## Output : TRUE
## Usage : _setPeak_ANNOTATION_IS_A_METABOLITE ( $VALUE ) ;

AUTHOR

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

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

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

Initiated by Franck Giacomoni

followed by INRAE PFEM team

Web Site = INRAE 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.

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