# MSEA by Subramanian et al. This function performs metabolite set enrichment analysis implemented in the same fashion as gene set enrichment analysis (Subramanian et al. 2005). In this function, a permutation procedure is performed for a metabolite set rather than class label. This procedure corresponds to a "gene set" of permutation type in GSEA-P software (Subramanian et al. 2007). A leading-edge subset analysis is also undertaken following the standard GSEA procedure. ```r msea_sub(M, D, y, maxiter = 1000) ``` ## Arguments - `M`: list of metbolite set name and metabolite IDs - `D`: data.frame(metabolite ID, data matix) - `y`: response variable (e.g. PC score) - `maxiter`: maximum number of iterations in random permutation (default=1000) ## Returns list of normalized enrichment score, p-value and q-value for metabolite set, and the results of leading edge subset ## References Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550. Subramanian, A., Kuehn, H., Gould, J., Tamayo, P., Mesirov, J.P. (2007) GSEA-P: A desktop application for Gene Set Enrichment Analysis. Bioinformatics, doi: 10.1093/bioinformatics/btm369. ## Author(s) Hiroyuki Yamamoto ## Examples ```r data(fasting) data(pathway) # pca and pca loading pca <- prcomp(fasting$X, scale=TRUE) pca <- pca_loading(pca) # all detected metabolites metabolites <- colnames(fasting$X) # statistically significant negatively correlated metabolites in PC1 loading SIG <- metabolites[pca$loading$R[,1] < 0 & pca$loading$p.value[,1] < 0.05] ALL <- metabolites #all detected metabolites # Set response variable y <- pca$x[,1] # preparing dataframe D <- data.frame(ALL,t(fasting$X)) # preparing dataframe M <- pathway$fasting P <- msea_sub(M,D,y, maxiter = 10) # iteration was set ato 10 for demonstration ```

msea_sub function