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 sensitivity RV coefficient (SRVC) miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, modulegenes_WGCNA, method = "SRVC", SMC.cutoff = 0.01, RV_method = "RV") miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]] miRSM_WGCNA_share_miRs <- share_miRs(miRExp, ceRExp, mRExp, miRTarget, miRSM_WGCNA_SRVC_genes)