module_Coexpress: module_Coexpress

In zhangjunpeng411/miRSM: Inferring miRNA sponge modules in heterogeneous data

module_Coexpress

Description

Co-expression analysis of each miRNA sponge module and its corresponding random miRNA sponge modules

Usage

module_Coexpress(
  ceRExp,
  mRExp = NULL,
  Modulelist,
  resample = 1000,
  method = c("mean", "median"),
  test.method = c("t.test", "wilcox.test")
)

Arguments

ceRExp	A SummarizedExperiment object. ceRNA expression data: rows are samples and columns are ceRNAs.
mRExp	NULL (default) or 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.

Value

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.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng-Zhang-2)

Examples

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")

zhangjunpeng411/miRSM documentation built on Feb. 9, 2024, 6:14 p.m.