Translate object properties to original options syntax



S = getCommand(optionsObject) returns a string S representing the modified properties in optionsObject translated into the original syntax (prefixed by one or two dashes) [1]. By default, the function translates only the modified properties. However, if the IncludeAll property of the object is set to true, the function translates all available properties, with default values for unspecified properties.


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Create a CufflinksOptions object.


getCommand also works on other cufflinks-related options objects, such as CuffDiffOptions, CuffCompareOptions, and CuffQuantOptions. For a complete list of objects, see optionsObject.

opt = CufflinksOptions;

Modify the object properties. For this example, specify the minimum average coverage for 3' end trimming and change the seed for the Cufflinks random number generator.

opt.TrimCoverageThreshold = 5;
opt.Seed = 1;

Retrieve the options translated into the original syntax.

s = getCommand(opt)
ans =

    "--seed -2.3 --trim-3-avgcov-thresh 5"

Input Arguments

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Output Arguments

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Options in the original syntax, returned as a string.


[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.

Introduced in R2019a