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"), test.method = c("t.test", "wilcox.test") )
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. |
test.method |
The method used to evaluate statistical significance p-value of co-expression level higher than random miRNA sponge modules. Users can select "t.test" or "wilcox.test" to calculate statistical significance p-value of co-expression level higher than random miRNA sponge modules. |
List object: co-expression values of miRNA sponge modules and their corresponding random miRNA sponge modules, and statistical significance p-value of co-expression level higher than 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 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_Coexpress <- module_Coexpress(ceRExp, mRExp, miRSM_WGCNA_SRVC_genes, resample = 10, method = "mean", test.method = "t.test")