evaluateStability: Evaluate Results Stability.

Description Usage Arguments Details Value Author(s) References Examples

Description

Perform a final Stability check comparing the results from all iterations of the analysis.

Usage

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evaluateStability(wall, hall, params)

Arguments

wall

numeric matrix including the w results from all the iterations of the analysis

hall

numeric matrix including the h results from all the iterations of the analysis

params

list including all the parameters required for running tha analysis

Details

The function evaluates the results from all iterations by performing a silhouette check. A silhouette plot will also be plotted. This is one of the core functions included in the original mutSignatures R library, and in the WTSI MATLAB framework. This is an internal function.

Value

list including all results from the stability checks. This includes the most likely signatures (cen-troids) and exposures. All information for plotting the silhoueette plot will also be returned.

Author(s)

Damiano Fantini, damiano.fantini@gmail.com

References

More information and examples about mutational signature analysis can be found here:

  1. GitHub Repo: https://github.com/dami82/mutSignatures/

  2. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

  3. Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/

  4. Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6

  5. WTSI framework: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588146/

Examples

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# Obtain sample data
TMP <- mutSignatures:::getTestRunArgs("evaluateStability")
Y <- mutSignatures:::evaluateStability(wall = TMP$W, 
                                       hall = TMP$H, 
                                       params = TMP$params)

mutSignatures documentation built on Nov. 9, 2020, 9:06 a.m.