module_Coexpress: module_Coexpress

Description Usage Arguments Value Author(s) Examples

View source: R/miRSM.R

Description

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

Usage

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module_Coexpress(
  ceRExp,
  mRExp,
  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

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_Zhang3)

Examples

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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 Nov. 28, 2020, 7 a.m.