Package: MetabolSSMF 0.1.0

MetabolSSMF: Simplex-Structured Matrix Factorisation for Metabolomics Analysis

Provides a framework to perform soft clustering using simplex-structured matrix factorisation (SSMF). The package contains a set of functions for determining the optimal number of prototypes, the optimal algorithmic parameters, the estimation confidence intervals and the diversity of clusters. Abdolali, Maryam & Gillis, Nicolas (2020) <doi:10.1137/20M1354982>.

Authors:Wenxuan Liu [aut, cre], Thomas Brendan Murphy [aut], Lorraine Brennan [aut]

MetabolSSMF_0.1.0.tar.gz
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MetabolSSMF.pdf |MetabolSSMF.html✨
MetabolSSMF/json (API)

# Install 'MetabolSSMF' in R:

install.packages('MetabolSSMF', repos = c('https://wenxuanliu1996.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wenxuanliu1996/metabolssmf/issues

Datasets:

SimulatedDataset - A simulated metabolomic dataset.
SimulatedMemberships - A simulated membership matrix.
SimulatedPrototypes - A simulated prototype matrix.
fit_SSMF - Example results of SSMF.
fit_boot - Example results of bootstrap.
fit_gap - Example results of gap statistic.

On CRAN:

4.18 score 6 exports 55 dependencies

Last updated 27 days agofrom:847c65f337. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 06 2025
R-4.5-win	OK	Mar 06 2025
R-4.5-mac	OK	Mar 06 2025
R-4.5-linux	OK	Mar 06 2025
R-4.4-win	OK	Mar 06 2025
R-4.4-mac	OK	Mar 06 2025
R-4.4-linux	OK	Mar 06 2025
R-4.3-win	OK	Mar 06 2025
R-4.3-mac	OK	Mar 06 2025

Exports:bootstrap diversity gap init sARI ssmf

Dependencies:Biobase BiocGenerics BiocManager cli cluster codetools colorspace cpp11 digest doParallel dplyr fansi farver foreach generics ggplot2 glue gridBase gtable isoband iterators labeling LaplacesDemon lattice lifecycle lsei magrittr MASS Matrix mclust mgcv munsell nlme NMF pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp registry reshape2 rlang rngtools scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

MetabolSSMF

Rendered fromMetabolSSMF.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-03-04
Started: 2025-02-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bootstrap algorithm function.	bootstrap
Shannon diversity index	diversity
Example results of bootstrap.	fit_boot
Example results of gap statistic.	fit_gap
Example results of SSMF.	fit_SSMF
Gap statistic algorithm.	gap
Initialise the membership matrix H or prototype matrix W.	init
Soft adjusted Rand index.	sARI
A simulated metabolomic dataset.	SimulatedDataset
A simulated membership matrix.	SimulatedMemberships
A simulated prototype matrix.	SimulatedPrototypes
Simplex-structured matrix factorisation algorithm (SSMF).	ssmf