module_CEA {miRSM} | R Documentation |
Cancer enrichment analysis of miRNA sponge modules using hypergeometric distribution test
module_CEA(ceRExp, mRExp, Cancergenes, Modulelist)
ceRExp |
A SummarizedExperiment object. ceRNA expression data: rows are samples and columns are ceRNAs. |
mRExp |
A SummarizedExperiment object. mRNA expression data: rows are samples and columns are mRNAs. |
Cancergenes |
A SummarizedExperiment object: a list of cancer genes given. |
Modulelist |
List object: a list of the identified miRNA sponge modules. |
Cancer enrichment significance p-values of the identified miRNA sponge modules
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
Johnson NL, Kotz S, Kemp AW (1992) "Univariate Discrete Distributions", Second Edition. New York: Wiley.
data(BRCASampleData) modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) # Identify miRNA sponge modules using canonical correlation (CC) miRSM_WGCNA_CC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, modulegenes_WGCNA, nperms = 10, method = 'CC') miRSM_WGCNA_CC_genes <- miRSM_WGCNA_CC[[2]] miRSM.CEA.pvalue <- module_CEA(ceRExp, mRExp, BRCA_genes, miRSM_WGCNA_CC_genes)