silhouetteMLB {mutSignatures}

Silhouette Analysis.

Description

Analyze the clustering quality and generate a Silhouette Plot.

Usage

silhouetteMLB(data, fac, method = "cosine", plot = TRUE)

Arguments

data

numeric matrix

fac

clustering factor

method

method to be used as distance function. Defaults to c("cosine")

plot

logical, shall a barplot showing the cluster silhouettes be printed

Value

numeric vector including the silhouette values of the data poointts in the input matrix

Author(s)

Damiano Fantini, [e-mail]

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. Silhouette analysis in R: http://www.biotechworld.it/bioinf/2017/01/20/translating-matlabs-silhouette-function-to-r/

Examples

library(mutSignatures)
x <- mutSignatures:::getTestRunArgs("silhouetteMLB")
y <- silhouetteMLB(data = x$data, fac = x$fac)
y