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MetabolSSMF

Simplex-structure matrix factorisation: application of soft clustering to metabolomics data

The package is built upon the 'Biobase' package from 'Bioconductor.' Before installing 'MetabolSSMF,' please ensure that 'Biobase' is installed by following the provided instructions.

Install the package

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("Biobase")

devtools::install_github("WenxuanLiu1996/MetabolSSMF")

Load the package

library(MetabolSSMF)

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Version

Install

install.packages('MetabolSSMF')

Version

0.1.0

License

MIT + file LICENSE

Maintainer

Wenxuan Liu

Last Published

March 5th, 2025

Functions in MetabolSSMF (0.1.0)

bootstrap

Bootstrap algorithm function.
fit_SSMF

Example results of SSMF.
SimulatedPrototypes

A simulated prototype matrix.
gap

Gap statistic algorithm.
init

Initialise the membership matrix \(H\) or prototype matrix \(W\).
diversity

Shannon diversity index
sARI

Soft adjusted Rand index.
ssmf

Simplex-structured matrix factorisation algorithm (SSMF).
SimulatedMemberships

A simulated membership matrix.
SimulatedDataset

A simulated metabolomic dataset.
fit_boot

Example results of bootstrap.
fit_gap

Example results of gap statistic.