/mseapca

R package for principal component analysis and metabolite set enrichment analysis

Primary LanguageR

mseapca

Metabolite set enrichment analysis for loadings

mseapca provides functions for metabolite set enrichment analysis with loading in principal component anaysis and partial least squares, and single sample enrichment analysis.

  • Metabolite set enrichment analysis [1] can be performed using the "msea_ora" or "msea_sub" functions.

  • Our mseapca package utilizes the loadings package ( https://cran.r-project.org/web/packages/loadings ) to conduct multivariate analyses like PCA and PLS, along with their respective loadings.

  • The "ssea_ora" function can be used to compute single sample enrichment analysis based on over-representation analysis [2].

  • Our mseapca package can incorporate a metabolite set list from the PathBank database by referencing the AHPathbankDbs Bioconductor package or through user-generated lists.

References
[1] Yamamoto H. et al., BMC Bioinformatics, (2014) 15(1):51. doi: https://doi.org/10.1186/1471-2105-15-51
[2] Yamamoto H. , Jxiv, (2023). doi: https://doi.org/10.51094/jxiv.484

Installation (in preparation)

The latest stable version can be installed from CRAN:

install.packages("mseapca")

The latest development version can be installed from GitHub:

# install.packages("devtools")
devtools::install_github("hiroyukiyamamoto/mseapca")