module_Coexpress {miRSM} | R Documentation |
Co-expression analysis of each miRNA sponge module and its corresponding random miRNA sponge module
module_Coexpress(ceRExp, mRExp, Modulelist, resample = 1000, method = c("mean", "median"))
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. |
Modulelist |
List object: a list of the identified miRNA sponge modules. |
resample |
The number of random miRNA sponge modules generated, and 1000 times in default. |
method |
The method used to evaluate the co-expression level of each miRNA sponge module. Users can select "mean" or "median" to calculate co-expression value of each miRNA sponge module and its corresponding random miRNA sponge module. |
List object: co-expression values of miRNA sponge modules and their corresponding random miRNA sponge modules.
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_Coexpress <- module_Coexpress(ceRExp, mRExp, miRSM_WGCNA_CC_genes, resample = 10, method = "mean")