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
MetabolSSMF_0.1.0.zip(r-4.7)MetabolSSMF_0.1.0.zip(r-4.6)MetabolSSMF_0.1.0.zip(r-4.5)
MetabolSSMF_0.1.0.tgz(r-4.6-any)MetabolSSMF_0.1.0.tgz(r-4.5-any)
MetabolSSMF_0.1.0.tar.gz(r-4.7-any)MetabolSSMF_0.1.0.tar.gz(r-4.6-any)
MetabolSSMF_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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:

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

On CRAN:

3.70 score 5 scripts 239 downloads 6 exports 49 dependencies

Last updated from:847c65f337. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	198
source / vignettes	OK	300
linux-release-x86_64	OK	175
macos-release-arm64	OK	166
macos-oldrel-arm64	OK	167
windows-devel	OK	108
windows-release	OK	108
windows-oldrel	OK	104
wasm-release	OK	167

Exports:bootstrap diversity gap init sARI ssmf

Dependencies:Biobase BiocGenerics BiocManager cli cluster codetools colorspace cpp11 digest doParallel dplyr farver foreach generics ggplot2 glue gridBase gtable isoband iterators labeling LaplacesDemon lifecycle lsei magrittr mclust NMF pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp registry reshape2 rlang rngtools S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

MetabolSSMF

Rendered fromMetabolSSMF.Rmdusingknitr::rmarkdown

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