mutSignatures (version 2.1.1)

silhouetteMLB: 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

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

# NOT RUN {
library(mutSignatures)
x <- mutSignatures:::getTestRunArgs("silhouetteMLB")
y <- silhouetteMLB(data = x$data, fac = x$fac)
y

# }