share_miRs {miRSM} | R Documentation |
Extract common miRNAs of each miRNA sponge module
share_miRs(miRExp, ceRExp, mRExp, miRTarget, Modulelist)
miRExp |
A SummarizedExperiment object. miRNA expression data: rows are samples and columns are miRNAs. |
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. |
miRTarget |
A SummarizedExperiment object. Putative miRNA-target binding information. |
Modulelist |
List object: a list of the identified miRNA sponge modules. |
List object: a list of common miRNAs of each miRNA sponge module.
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
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_WGCNA_share_miRs <- share_miRs(miRExp, ceRExp, mRExp, miRTarget, miRSM_WGCNA_CC_genes)