mutSignatures (version 2.1.1)

evaluateStability: Evaluate Results Stability.

Description

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

Usage

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

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.

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.

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

# NOT RUN {
# Obtain sample data
TMP <- mutSignatures:::getTestRunArgs("evaluateStability")
Y <- mutSignatures:::evaluateStability(wall = TMP$W, 
                                       hall = TMP$H, 
                                       params = TMP$params)


# }