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].

• The “msea_ora” function performs over-representation analysis while accounting for undetected metabolites [3].

• The “msea_ora_range” function estimates the possible range of p-values under uncertainty caused by undetected metabolites [3].

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 [3] Yamamoto H. , Jxiv, (2024). doi: https://doi.org/10.51094/jxiv.954

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")