Main Content

getCommand

Translate object properties to original options syntax

collapse all in page

Syntax

S = getCommand(optionsObject)

Description

S = getCommand(optionsObject) returns a string S representing the modified properties in optionsObject translated into the original syntax (prefixed by one or two dashes). By default, the function translates only the modified properties.

Note

If you set IncludeAll to true, the software converts all available properties, using default values for unspecified properties. The only exception is when the default value of a property is NaN, Inf, [], '', or "". In this case, the software does not translate the corresponding property.

example

Examples

collapse all

Create a CufflinksOptions object.

Note

getCommand also works on other options objects. 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

collapse all

Options, specified as a BWAIndexOptions, BWAMEMOptions, CufflinksOptions, CuffCompareOptions, CuffMergeOptions, CuffQuantOptions, CuffDiffOptions, CuffNormOptions, or CuffGFFReadOptions object.

Output Arguments

collapse all

Options in the original syntax, returned as a string.

References

[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. https://doi.org/10.1093/bioinformatics/btp324.

[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. https://doi.org/10.1093/bioinformatics/btp698.

Version History

Introduced in R2019a

See Also

| | | | | | |