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Return table with all properties and equivalent options in original syntax



tbl = getOptionsTable(optionsObject) returns a table with all the object properties and equivalent options in the original (native) syntax.


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Create a CufflinksOptions object.


getOptionsTable also works on other options objects. For a complete list of objects, see optionsObject.

opt = CufflinksOptions;

Retrieve the equivalent original options for all object properties.

ans =

  35×3 table

                                        PropertyName                         FlagName                 FlagShortName
                                 ___________________________    __________________________________    _____________

    EffectiveLengthCorrection    'EffectiveLengthCorrection'    '--no-effective-length-correction'        ''       
    FauxReadTiling               'FauxReadTiling'               '--no-faux-reads'                         ''       
    FragmentBiasCorrection       'FragmentBiasCorrection'       '--frag-bias-correct'                     '-b'     
    FragmentLengthMean           'FragmentLengthMean'           '--frag-len-mean'                         '-m'     
    FragmentLengthSTD            'FragmentLengthSTD'            '--frag-len-std-dev'                      '-s'     
    GTFGuide                     'GTFGuide'                     '--GTF-guide'                             '-g'     
    IntronOverhangTolerance      'IntronOverhangTolerance'      '--intron-overhang-tolerance'             ''       
    JunctionAlpha                'JunctionAlpha'                '--junc-alpha'                            '-a'     
    LengthCorrection             'LengthCorrection'             '--no-length-correction'                  ''       
    MaskFile                     'MaskFile'                     '--mask-file'                             '-M'     
    MaxBundleFrags               'MaxBundleFrags'               '--max-bundle-frags'                      ''       
    MaxBundleLength              'MaxBundleLength'              '--max-bundle-length'                     ''       
    MaxFragAlignments            'MaxFragAlignments'            '--max-frag-multihits'                    ''       
    MaxIntronLength              'MaxIntronLength'              '--max-intron-length'                     '-I'     
    MaxMLEIterations             'MaxMLEIterations'             '--max-mle-iterations'                    ''       
    MinFragsPerTransfrag         'MinFragsPerTransfrag'         '--min-frags-per-transfrag'               ''       
    MinIntronLength              'MinIntronLength'              '--min-intron-length'                     ''       
    MinIsoformFraction           'MinIsoformFraction'           '--min-isoform-fraction'                  '-F'     
    MultiReadCorrection          'MultiReadCorrection'          '--multi-read-correct'                    '-u'     
    NormalizeCompatibleHits      'NormalizeCompatibleHits'      '--compatible-hits-norm'                  ''       
    NormalizeTotalHits           'NormalizeTotalHits'           '--total-hits-norm'                       ''       
    NumFragAssignmentSamples     'NumFragAssignmentSamples'     '--num-frag-assign-draws'                 ''       
    NumFragSamples               'NumFragSamples'               '--num-frag-count-draws'                  ''       
    NumThreads                   'NumThreads'                   '--num-threads'                           '-p'     
    OutputDirectory              'OutputDirectory'              '--output-dir'                            '-o'     
    OverhangTolerance            'OverhangTolerance'            '--overhang-tolerance'                    ''       
    OverhangTolerance3           'OverhangTolerance3'           '--3-overhang-tolerance'                  ''       
    OverlapRadius                'OverlapRadius'                '--overlap-radius'                        ''       
    PreMRNAFraction              'PreMRNAFraction'              '--pre-mrna-fraction'                     '-j'     
    ReferenceGTF                 'ReferenceGTF'                 '--GTF'                                   '-G'     
    Seed                         'Seed'                         '--seed'                                  ''       
    SmallAnchorFraction          'SmallAnchorFraction'          '--small-anchor-fraction'                 '-A'     
    TranscriptPrefix             'TranscriptPrefix'             '--label'                                 '-L'     
    TrimCoverageThreshold        'TrimCoverageThreshold'        '--trim-3-avgcov-thresh'                  ''       
    TrimDropoffFraction          'TrimDropoffFraction'          '--trim-3-dropoff-frac'                   ''       

Input Arguments

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Output Arguments

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Object properties and their corresponding original options, returned as a table.


[1] Trapnell, C., B. Williams, G. Pertea, A. Mortazavi, G. Kwan, J. van Baren, S. Salzberg, B. Wold, and L. Pachter. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology. 28:511–515.

[2] Li, Heng, and Richard Durbin. “Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform.” Bioinformatics 25, no. 14 (July 15, 2009): 1754–60.

[3] Li, Heng, and Richard Durbin. “Fast and Accurate Long-Read Alignment with Burrows–Wheeler Transform.” Bioinformatics 26, no. 5 (March 1, 2010): 589–95.

Version History

Introduced in R2019a