NAME

Metabolomics::Utils - Perl Utils extension metabolomics::fragment::annotation module

VERSION

Version 0.2 - Adding POD Version 0.3 - Adding Scoring methods for gcms annotation analysis Version 0.4 - Adding RI computing

SYNOPSIS

    use Metabolomics::Utils;

DESCRIPTION

        Metabolomics::Utils is a module containing little helper as formatters, parsers, conf called during annotation steps 

EXPORT

        use Metabolomics::Utils;

PUBLIC METHODS

Metabolomics::Utils ;

new

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

roundFloat

        ## Description : round a float by the sended decimal
        ## Input : $number, $decimal
        ## Output : $round_num
        ## Usage : my ( $round_num ) = roundFloat( $number, $decimal ) ;

METHOD getSmallestDecimalPartOf2Numbers

        ## Description : get the smallest decimal part of two numbers
        ## Input : $float01, $float02
        ## Output : $commonLenghtDecimalPart
        ## Usage : my ( $commonLenghtDecimalPart ) = getSmallestDecimalPartOf2Numbers ( $float01, $float02 ) ;

METHOD validFloat

        ## Description : valid float as float with dot as decimal separator
        ## Input : $refFloats
        ## Output : \@floats 
        ## Usage : my ( \@floats ) = validFloat( $refFloats ) ;

METHOD trackZeroIntensity

        ## Description : track zero value in raw intensity
        ## Input : $refFloats
        ## Output : \@floats 
        ## Usage : my ( \@floats ) = trackZeroIntensity( $refFloats ) ;

METHOD computeScorePairedPeaksIntensitiesPearsonCorrelation

        ## Description : Pearson correlation between intensities of paired peaks, where unmatched peaks are paired with zero-intensity "pseudo-peaks"
        ## Input : $x
        ## Output : $correlation (<=1)
        ## Usage : my ( $correlation ) = computeScorePairedPeaksIntensitiesPearsonCorrelation ( $x ) ;

METHOD _computeScoreMatchedQueryPeaksPercent

        ## Description : Proportion of query peaks with matches. 
        ## Input : $nbMatches, $nbQueryPeaks
        ## Output : $scoreQ
        ## Usage : my ( $scoreQ ) = _computeScoreMatchedQueryPeaksPercent ( $nbMatches, $nbQueryPeaks ) ;

METHOD _computeScoreMatchedLibrarySpectrumPeaksPercent

        ## Description : Proportion of library spectrum's peaks with matches. 
        ## Input : $nbMatches, $nbLibPeaks
        ## Output : $scoreL
        ## Usage : my ( $scoreL ) = computeScoreMatchedLibrarySpectrumPeaksPercent ( $nbMatches, $nbLibPeaks ) ;

METHOD computeAbsoluteIntensitiesInRelativeIntensity100

        ## Description : compute a whole liste of relative Intensity (100-based) 
        ## Input : $mz_res, $ints_res
        ## Output : $relative_ints
        ## Usage : my ( $relative_ints ) = computeAbsoluteIntensitiesInRelativeIntensity100 ( $mz_res, $ints_res ) ;

utilsAsConf

        ## Description : build a conf from a conf file with KEY=VALUE structure
        ## Input : $file
        ## Ouput : $oConf (a hash)
        ## Usage : my ( $oConf ) = utilsAsConf( $file ) ;

AUTHOR

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

SEE ALSO

All information about Metabolomics::Banks 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::Utils

• 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 INRA PFEM team

Web Site = INRA PFEM