Metabolomics::Fragment::Annotation - Perl extension for fragment annotation in metabolomics
Version 0.4
use Metabolomics::Fragment::Annotation;
Metabolomics::Fragment::Annotation is a full package for Perl dev allowing MS fragments annotation with ab initio database, contaminant and public metabolites ressources.
## Description : new ## Input : $self ## Ouput : bless $self ; ## Usage : new() ;
## Description : comparing two lists of mzs (theo and experimental) with a mz delta ## Input : $deltaValue, $deltaType ## Output : $oAnalysis with annotation results ## Usage : $oAnalysis->compareExpMzToTheoMzList ( $deltaValue, $deltaType ) ;
## Description : write a full tabular file from a template and mapping peak bank objects features ## Input : $oBank, $templateTabular, $tabular ## Output : $tabular ## Usage : my ( $tabular ) = $oBank->writeTabularWithPeakBankObject ( $templateTabular, $tabular ) ;
## Description : write a output containing the input data and new column concerning annotation work ## Input : $oBank, $inputData, $templateTabular, $tabular ## Output : $tabular ## Usage : my ( $tabular ) = $oBank->writeFullTabularWithPeakBankObject ( $inputData, $templateTabular, $tabular ) ;
## Description : get a specific list of peaks from the Annotation analysis object ## Input : $self, $type ## Output : $peakList ## Usage : my ( $peakList ) = $oAnalysis->_getPeakList ($type) ;
## Description : get all fields of the tabular template file ## Input : $template ## Output : $fields ## Usage : my ( $fields ) = _getTEMPLATE_TABULAR_FIELDS ( $template ) ;
## Description : map any PeakList with any template fields from tabular ## Input : $fields, $peakList ## Output : $rows ## Usage : my ( $rows ) = _mapPeakListWithTemplateFields ( $fields, $peakList ) ;
## Description : returns the minimum and maximum mass according to the delta ## Input : \$mass, \$delta_type, \$mz_delta ## Output : \$min, \$max ## Usage : ($min, $max)= mz_delta_conversion($mass, $delta_type, $mz_delta) ;
## Description : compute a delta (Da) between exp. mz and calc. mz ## based on http://www.waters.com/waters/en_GB/Mass-Accuracy-and-Resolution/nav.htm?cid=10091028&locale=en_GB ## Other ref : https://www.sciencedirect.com/science/article/pii/S1044030510004022 ## Input : $expMz, $calcMz ## Output : $mzDeltaDa ## Usage : my ( $mzDeltaDa ) = _computeMzDeltaInMmu ( $expMz, $calcMz ) ;
## Description : compute a delta (PPM) between exp. mz and calc. mz - Δm/Monoisotopic calculated exact mass ×106 ## Input : $expMz, $calcMz ## Output : $mzDeltaPpm ## Usage : my ( $mzDeltaPpm ) = computeMzDeltaInPpm ( $expMz, $calcMz ) ;
Franck Giacomoni, <franck.giacomoni at inra.fr>
<franck.giacomoni at inra.fr>
All information about FragNot should be find here: https://services.pfem.clermont.inra.fr/gitlab/fgiacomoni/fragnot
Please report any bugs or feature requests to bug-metabolomics-fragnot at rt.cpan.org, or through the web interface at https://rt.cpan.org/NoAuth/ReportBug.html?Queue=Metabolomics-FragNot. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
bug-metabolomics-fragnot at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Metabolomics::Fragment::Annotation
RT: CPAN's request tracker (report bugs here)
https://rt.cpan.org/NoAuth/Bugs.html?Dist=Metabolomics-FragNot
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Metabolomics-FragNot
CPAN Ratings
https://cpanratings.perl.org/d/Metabolomics-FragNot
Search CPAN
https://metacpan.org/release/Metabolomics-FragNot
CeCILL Copyright (C) 2019 by Franck Giacomoni
Initiated by Franck Giacomoni
followed by INRA PFEM team
Web Site = INRA PFEM
1 POD Error
The following errors were encountered while parsing the POD:
Non-ASCII character seen before =encoding in 'Δm/Monoisotopic'. Assuming CP1252
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.