diff --git a/man/BRCA_genes.Rd b/man/BRCA_genes.Rd
new file mode 100644
index 0000000..3d00c02
--- /dev/null
+++ b/man/BRCA_genes.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{BRCA_genes}
+\alias{BRCA_genes}
+\title{BRCA genes}
+\format{
+BRCA_genes: A SummarizedExperiment object with
+4819 BRCA related genes (including lncRNAs and mRNAs).
+}
+\description{
+BRCA genes
+}
+\details{
+The BRCA related lncRNAs are from LncRNADisease v2.0, Lnc2Cancer v2.0 
+and MNDR v2.0. The BRCA related mRNAs are from DisGeNET v5.0 and COSMIC v86.
+}
+\references{
+Bao Z, Yang Z, Huang Z, Zhou Y, Cui Q, Dong D. (2019) 
+"LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases".
+Nucleic Acids Res., 47(D1):D1034-D1037.
+
+Cui T, Zhang L, Huang Y, Yi Y, Tan P, Zhao Y, Hu Y, Xu L, Li E, Wang D. 
+(2018) "MNDR v2.0: an updated resource of ncRNA-disease 
+associa-tions in mammals". Nucleic Acids Res., 46, D371-D374.
+
+Gao Y, Wang P, Wang Y, Ma X, Zhi H, Zhou D, Li X, Fang Y, Shen W, Xu Y, 
+Shang S, Wang L, Wang L, Ning S, Li X. (2019) "Lnc2Cancer v2.0: updated database of experimentally 
+supported long non-coding RNAs in human cancers". Nucleic Acids Res., 47, D1028-D1033.
+
+Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, 
+Ward S, Dawson E, Ponting L, Stefancsik R, Harsha B, Kok CY, Jia M, Jubb H, Sondka Z, 
+Thompson S, De T, Campbell PJ. (2017) "COSMIC: somatic cancer genetics at 
+high-resolution". Nucleic Acids Res., 45, D777-D783
+
+Pinero J, Bravo A, Queralt-Rosinach N, Gutierrez-Sacristan A, Deu-Pons J, 
+Centeno E, Garcia-Garcia J, Sanz F, Furlong LI. 
+(2017) "DisGeNET: a comprehensive platform integrating 
+infor-mation on human disease-associated genes and variants". 
+Nucleic Acids Res., 45, D833-D839.
+}
diff --git a/man/ceRExp.Rd b/man/ceRExp.Rd
new file mode 100644
index 0000000..f987d54
--- /dev/null
+++ b/man/ceRExp.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{ceRExp}
+\alias{ceRExp}
+\title{ceRNA expression data}
+\format{
+ceRExp: A SummarizedExperiment object with 72 BRCA 
+and 72 normal samples (rows) and 305 lncRNAs (columns).
+}
+\description{
+ceRNA expression data
+}
+\details{
+The matched breast invasive carcinoma (BRCA) miRNA, lncRNA 
+and mRNA expression data is obtained from TCGA 
+(http://cancergenome.nih.gov/). lncRNA expression data 
+is regarded as ceRNA expression data. The data focuses on 
+72 individuals for which the complete sets of 
+tumor and matched normal (i.e., normal tissue taken from the 
+same patient) profiles are available. 
+A lncRNA which has missing values in more than 
+10% of the samples is removed. The remaining missing values
+are imputed using the k-nearest neighbours (KNN) algorithm
+from the impute R package. We use the limma R package
+to infer differentially expressed lncRNAs
+between tumour and normal samples. After the analysis, 
+we select top 305 lncRNAs which are differentially expressed
+at a significant level (adjusted p-value < 1E-02,  
+adjusted by Benjamini & Hochberg method).
+}
diff --git a/man/cor_binary.Rd b/man/cor_binary.Rd
new file mode 100644
index 0000000..235707b
--- /dev/null
+++ b/man/cor_binary.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{cor_binary}
+\alias{cor_binary}
+\title{cor_binary}
+\usage{
+cor_binary(
+  ceRExp,
+  mRExp = NULL,
+  cor.method = "pearson",
+  pos.p.value.cutoff = 0.01
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{cor.method}{The method of calculating correlation selected, 
+including 'pearson' (default), 'kendall', 'spearman'.}
+
+\item{pos.p.value.cutoff}{The significant p-value cutoff of 
+positive correlation.}
+}
+\value{
+A binary matrix.
+}
+\description{
+Generation of positively correlated binary matrix between 
+ceRNAs, or ceRNAs and mRNAs
+}
+\examples{
+data(BRCASampleData)
+cor_binary_matrix <- cor_binary(ceRExp, mRExp)
+
+}
+\references{
+Langfelder P, Horvath S. WGCNA: an R package for 
+weighted correlation network analysis. BMC Bioinformatics. 
+2008, 9:559.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/diff_module.Rd b/man/diff_module.Rd
new file mode 100644
index 0000000..010238c
--- /dev/null
+++ b/man/diff_module.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{diff_module}
+\alias{diff_module}
+\title{diff_module}
+\usage{
+diff_module(
+  Module.group1,
+  Module.group2,
+  sim.cutoff = 0.8,
+  sim.method = "Simpson"
+)
+}
+\arguments{
+\item{Module.group1}{List object, the first list of module group.}
+
+\item{Module.group2}{List object, the second list of module group.}
+
+\item{sim.cutoff}{Similarity cutoff between modules, the interval is [0 1].}
+
+\item{sim.method}{Methods for calculating similatiry between two modules, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.}
+}
+\value{
+A list of differential modules
+}
+\description{
+Inferring differential modules between two list of module groups
+}
+\examples{
+library(GSEABase)
+data(BRCASampleData)
+modulegenes_WGCNA_all <- module_WGCNA(ceRExp, mRExp)
+modulegenes_WGCNA_1 <- module_WGCNA(ceRExp[-1, ], mRExp[-1, ])
+Differential_module <- diff_module(geneIds(modulegenes_WGCNA_all), geneIds(modulegenes_WGCNA_1))
+
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/mRExp.Rd b/man/mRExp.Rd
new file mode 100644
index 0000000..f4d190f
--- /dev/null
+++ b/man/mRExp.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{mRExp}
+\alias{mRExp}
+\title{mRNA expression data}
+\format{
+mRExp: A SummarizedExperiment 
+object with 72 BRCA and 72 normal samples (rows) and 226 miRNAs 
+(columns).
+}
+\description{
+mRNA expression data
+}
+\details{
+The matched breast invasive carcinoma (BRCA) miRNA, lncRNA 
+and mRNA expression data is obtained from TCGA 
+(http://cancergenome.nih.gov/). The data focuses on 
+72 individuals for which the complete sets of 
+tumor and matched normal (i.e., normal tissue taken from the 
+same patient) profiles are available. 
+A mRNA which has missing values in more than 
+10% of the samples is removed. The remaining missing values
+are imputed using the k-nearest neighbours (KNN) algorithm
+from the impute R package. We use the limma R package
+to infer differentially expressed mRNAs
+between tumour and normal samples. After the analysis, 
+we select top 500 mRNAs which are differentially expressed
+at a significant level (adjusted p-value < 1E-02,  
+adjusted by Benjamini & Hochberg method).
+}
diff --git a/man/miRExp.Rd b/man/miRExp.Rd
new file mode 100644
index 0000000..5103527
--- /dev/null
+++ b/man/miRExp.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{miRExp}
+\alias{miRExp}
+\title{miRNA expression data}
+\format{
+miRExp: A SummarizedExperiment object with 72 BRCA and 72 normal
+samples (rows) and 226 miRNAs (columns).
+}
+\description{
+miRNA expression data
+}
+\details{
+The matched breast invasive carcinoma (BRCA) miRNA, lncRNA 
+and mRNA expression data is obtained from TCGA 
+(http://cancergenome.nih.gov/). The data focuses on 
+72 individuals for which the complete sets of 
+tumor and matched normal (i.e., normal tissue taken from the 
+same patient) profiles are available. 
+A miRNA which has missing values in more than 
+10% of the samples is removed. The remaining missing values
+are imputed using the k-nearest neighbours (KNN) algorithm
+from the impute R package. We use the limma R package
+to infer differentially expressed miRNAs, ceRNAs and mRNAs
+between tumour and normal samples. After the analysis, 
+we select top 226 miRNAs which are differentially expressed 
+at a significant level (adjusted p-value < 1E-02,  
+adjusted by Benjamini & Hochberg method).
+}
diff --git a/man/miRSM.Rd b/man/miRSM.Rd
new file mode 100644
index 0000000..51bc93d
--- /dev/null
+++ b/man/miRSM.Rd
@@ -0,0 +1,151 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{miRSM}
+\alias{miRSM}
+\title{miRSM}
+\usage{
+miRSM(
+  miRExp,
+  ceRExp,
+  mRExp = NULL,
+  miRTarget,
+  CandidateModulegenes,
+  typex = "standard",
+  typez = "standard",
+  nperms = 100,
+  method = c("SCC", "SDC", "SRVC", "SM", "SSI", "SGCD", "SCRC"),
+  num_shared_miRNAs = 3,
+  pvalue.cutoff = 0.05,
+  MC.cutoff = 0.8,
+  SMC.cutoff = 0.1,
+  RV_method = c("RV", "RV2", "RVadjMaye", "RVadjGhaziri"),
+  BCmethod = "BCPlaid",
+  CRC_method = c("Coxhead", "Rozeboom")
+)
+}
+\arguments{
+\item{miRExp}{A SummarizedExperiment object. miRNA expression data: 
+rows are samples and columns are miRNAs.}
+
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{miRTarget}{A SummarizedExperiment object. Putative 
+miRNA-target binding information.}
+
+\item{CandidateModulegenes}{List object: a list of candidate 
+miRNA sponge modules. Only for the SCC, SDC, SRVC, SSI, SGCD and SCRC methods.}
+
+\item{typex}{The columns of x unordered (type='standard') or 
+ordered (type='ordered'). Only for the SCC method.}
+
+\item{typez}{The columns of z unordered (type='standard') or 
+ordered (type='ordered'). Only for the SCC method.}
+
+\item{nperms}{The number of permutations. Only for the SCC method.}
+
+\item{method}{The method selected to identify miRNA sponge 
+modules, including 'SCC', 'SDC', 'SRVC', 'SM', 'SSI', 'SGCD' and 'SCRC'.}
+
+\item{num_shared_miRNAs}{The number of common miRNAs shared 
+by a group of ceRNAs and mRNAs. Only for the SCC, SDC, SRVC, SSI, 
+SGCD and SCRC methods.}
+
+\item{pvalue.cutoff}{The p-value cutoff of significant sharing 
+of common miRNAs by a group of ceRNAs and mRNAs or significant correlation.}
+
+\item{MC.cutoff}{The cutoff of matrix correlation (canonical correlation, 
+distance correlation and RV coefficient). Only for the SCC, SDC, SRVC, 
+SSI, SGCD and SCRC methods.}
+
+\item{SMC.cutoff}{The cutoff of sensitivity matrix correlation
+(sensitivity canonical correlation, sensitivity distance correlation 
+and sensitivity RV coefficient). Only for the SCC, SDC, SRVC, SSI, 
+SGCD and SCRC methods.}
+
+\item{RV_method}{the method of calculating RV coefficients. Select
+one of 'RV', 'RV2', 'RVadjMaye' and 'RVadjGhaziri' methods.
+Only for the SRVC method.}
+
+\item{BCmethod}{Specification of the biclustering method, 
+including 'BCBimax', 'BCCC', 'BCPlaid' (default), 'BCQuest', 
+'BCSpectral', 'BCXmotifs'. Only for the SM method.}
+
+\item{CRC_method}{the method of calculating matrix correlation. Select
+one of 'Coxhead' and 'Rozeboom' methods.
+Only for the SCRC method.}
+}
+\value{
+List object: Group competition of miRNA sponge modules,
+and miRNA sponge modules.
+}
+\description{
+Identify miRNA sponge modules using sensitivity canonical correlation (SCC), 
+sensitivity distance correlation (SDC),
+sensitivity RV coefficient (SRVC), sensitivity similarity index (SSI), 
+sensitivity generalized coefficient of determination (SGCD), 
+sensitivity Coxhead's or Rozeboom's coefficient (SCRC), 
+and sponge module (SM) methods.
+}
+\examples{
+data(BRCASampleData)
+modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], 
+    mRExp[, seq_len(10)])
+# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC)
+miRSM_igraph_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget,
+                        modulegenes_igraph, method = "SRVC",
+                        SMC.cutoff = 0.01, RV_method = "RV")
+
+}
+\references{
+Witten DM, Tibshirani R, Hastie T. A penalized matrix 
+decomposition, with applications to sparse principal components 
+and canonical correlation analysis. Biostatistics. 
+2009, 10(3):515-34.
+
+Szekely GJ, Rizzo ML. Partial distance 
+correlation with methods for dissimilarities. Annals of Statistics. 
+2014, 42(6):2382-2412.
+
+Szekely GJ, Rizzo ML, Bakirov NK. 
+Measuring and Testing Dependence by Correlation of Distances, 
+Annals of Statistics, 2007, 35(6):2769-2794.
+
+Robert P, Escoufier Y. A unifying tool for 
+linear multivariate statistical methods: the RV-Coefficient. 
+Applied Statistics, 1976, 25(3):257-265.
+
+Smilde AK, Kiers HA, Bijlsma S, Rubingh CM, 
+van Erk MJ. Matrix correlations for high-dimensional 
+data: the modified RV-coefficient. Bioinformatics, 
+2009, 25(3):401-405.
+
+Maye CD, Lorent J, Horgan GW. 
+Exploratory analysis of multiple omics datasets using 
+the adjusted RV coefficient". Stat Appl Genet Mol Biol., 
+2011, 10, 14.
+
+EIGhaziri A, Qannari EM. Measures 
+of association between two datasets; Application to sensory data, 
+Food Quality and Preference, 2015, 40(A):116-124.
+
+Indahl UG, Næs T, Liland KH. A similarity index for 
+comparing coupled matrices. Journal of Chemometrics. 2018; 32:e3049.
+
+Yanai H. Unification of various techniques of multivariate 
+analysis by means of generalized coefficient of determination (GCD). 
+Journal of Behaviormetrics, 1974, 1(1): 45-54.
+
+Coxhead P. Measuring the relationship between two sets 
+of variables. British journal of mathematical and statistical psychology, 
+1974, 27(2): 205-212.
+
+Rozeboom WW. Linear correlations between sets of variables.
+Psychometrika, 1965, 30(1): 57-71.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/miRSM_SS.Rd b/man/miRSM_SS.Rd
new file mode 100644
index 0000000..2945129
--- /dev/null
+++ b/man/miRSM_SS.Rd
@@ -0,0 +1,56 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{miRSM_SS}
+\alias{miRSM_SS}
+\title{miRSM_SS}
+\usage{
+miRSM_SS(
+  Modulelist.all,
+  Modulelist.exceptk,
+  sim.cutoff = 0.8,
+  sim.method = "Simpson"
+)
+}
+\arguments{
+\item{Modulelist.all}{List object, modules using all of samples.}
+
+\item{Modulelist.exceptk}{List object, modules using all of samples excepting sample k.}
+
+\item{sim.cutoff}{Similarity cutoff between modules, the interval is [0 1].}
+
+\item{sim.method}{Methods for calculating similatiry between two modules, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.}
+}
+\value{
+A list of sample-specific miRNA sponge modules
+}
+\description{
+Inferring sample-specific miRNA sponge modules
+}
+\examples{
+data(BRCASampleData)
+nsamples <- 3
+modulegenes_igraph_all <- module_igraph(ceRExp[, 151:300], mRExp[, 151:300])
+modulegenes_WGCNA_exceptk <- lapply(seq(nsamples), function(i) 
+                             module_WGCNA(ceRExp[-i, seq(150)], 
+                             mRExp[-i, seq(150)]))
+ 
+miRSM_igraph_SRVC_all <- miRSM(miRExp, ceRExp[, 151:300], mRExp[, 151:300], 
+                               miRTarget, modulegenes_igraph_all, 
+                               method = "SRVC", SMC.cutoff = 0.01, 
+                               RV_method = "RV")
+miRSM_WGCNA_SRVC_exceptk <- lapply(seq(nsamples), function(i) miRSM(miRExp[-i, ], 
+                                   ceRExp[-i,  seq(150)], mRExp[-i,  seq(150)], 
+                                   miRTarget, modulegenes_WGCNA_exceptk[[i]],#'                                     
+                                   method = "SRVC",
+                                   SMC.cutoff = 0.01, RV_method = "RV"))
+
+Modulegenes_all <- miRSM_igraph_SRVC_all[[2]]
+Modulegenes_exceptk <- lapply(seq(nsamples), function(i) 
+                              miRSM_WGCNA_SRVC_exceptk[[i]][[2]])
+
+Modules_SS <- miRSM_SS(Modulegenes_all, Modulegenes_exceptk)
+
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/miRTarget.Rd b/man/miRTarget.Rd
new file mode 100644
index 0000000..cae6ae7
--- /dev/null
+++ b/man/miRTarget.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{miRTarget}
+\alias{miRTarget}
+\title{miRNA-target ineractions}
+\format{
+miRTarget: A SummarizedExperiment object with
+29901 miRNA-target interactions.
+}
+\description{
+miRNA-target ineractions
+}
+\details{
+The miRNA-target binding information is
+from miRTarBase v8.0 (http://mirtarbase.mbc.nctu.edu.tw/php/index.php),
+and LncBase v2.0
+(http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2/index).
+Among 226 miRNAs, 305 lncRNAs and 500 mRNAs 
+which are differentially expressed, we obtain 29901 miRNA-target
+interactions (including miRNA-lncRNA and miRNA-mRNA interactions).
+}
+\references{
+Hastie T, Tibshirani R, Narasimhan B, Chu G. 
+impute: Imputation for microarray data. 
+R package version 1.54.0. doi:  10.18129/B9.bioc.impute.
+
+Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, 
+Shi W, et al. limma powers differential expression 
+analyses for RNA-sequencing and microarray studies. 
+Nucleic Acids Res. 2015; 43(7):e47.
+}
diff --git a/man/module_CEA.Rd b/man/module_CEA.Rd
new file mode 100644
index 0000000..90bc8f6
--- /dev/null
+++ b/man/module_CEA.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_CEA}
+\alias{module_CEA}
+\title{module_CEA}
+\usage{
+module_CEA(ceRExp, mRExp = NULL, Cancergenes, Modulelist)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{Cancergenes}{A SummarizedExperiment object: a list of cancer genes given.}
+
+\item{Modulelist}{List object: a list of the identified miRNA sponge modules.}
+}
+\value{
+Cancer enrichment significance p-values of the identified miRNA sponge modules
+}
+\description{
+Cancer enrichment analysis of miRNA sponge modules using hypergeometric distribution test
+}
+\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.CEA.pvalue <- module_CEA(ceRExp, mRExp, BRCA_genes, 
+                              miRSM_WGCNA_SRVC_genes)
+
+}
+\references{
+Johnson NL, Kotz S, Kemp AW (1992) 
+"Univariate Discrete Distributions", Second Edition. New York: Wiley.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_Coexpress.Rd b/man/module_Coexpress.Rd
new file mode 100644
index 0000000..aa43181
--- /dev/null
+++ b/man/module_Coexpress.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_Coexpress}
+\alias{module_Coexpress}
+\title{module_Coexpress}
+\usage{
+module_Coexpress(
+  ceRExp,
+  mRExp = NULL,
+  Modulelist,
+  resample = 1000,
+  method = c("mean", "median"),
+  test.method = c("t.test", "wilcox.test")
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{Modulelist}{List object: a list of the identified miRNA sponge modules.}
+
+\item{resample}{The number of random miRNA sponge modules generated, and 1000 times in default.}
+
+\item{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.}
+
+\item{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.
+}
+\description{
+Co-expression analysis of each miRNA sponge module and its corresponding random miRNA sponge modules
+}
+\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")
+
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_FA.Rd b/man/module_FA.Rd
new file mode 100644
index 0000000..3a7c2d5
--- /dev/null
+++ b/man/module_FA.Rd
@@ -0,0 +1,80 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_FA}
+\alias{module_FA}
+\title{module_FA}
+\usage{
+module_FA(
+  Modulelist,
+  GOont = "BP",
+  Diseaseont = "DO",
+  KEGGorganism = "hsa",
+  Reactomeorganism = "human",
+  OrgDb = "org.Hs.eg.db",
+  padjustvaluecutoff = 0.05,
+  padjustedmethod = "BH",
+  Analysis.type = c("FEA", "DEA")
+)
+}
+\arguments{
+\item{Modulelist}{List object: a list of miRNA sponge modules.}
+
+\item{GOont}{One of 'MF', 'BP', and 'CC' subontologies.}
+
+\item{Diseaseont}{One of 'DO', and 'DOLite' subontologies.}
+
+\item{KEGGorganism}{Organism, supported organism listed 
+in http://www.genome.jp/kegg/catalog/org_list.html.}
+
+\item{Reactomeorganism}{Organism, one of 'human', 'rat', '
+mouse', 'celegans', 'yeast', 'zebrafish', 'fly'.}
+
+\item{OrgDb}{OrgDb}
+
+\item{padjustvaluecutoff}{A cutoff value of adjusted p-values.}
+
+\item{padjustedmethod}{Adjusted method of p-values, can select 
+one of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 
+'fdr', 'none'.}
+
+\item{Analysis.type}{The type of functional analysis selected, 
+including 'FEA' (functional enrichment analysis) and 'DEA' 
+(disease enrichment analysis).}
+}
+\value{
+List object: a list of enrichment analysis results.
+}
+\description{
+Functional analysis of miRNA sponge modules, including functional 
+enrichment and disease enrichment analysis
+}
+\examples{
+\dontrun{
+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_SRVC_FEA <- module_FA(miRSM_WGCNA_SRVC_genes, Analysis.type = 'FEA')
+miRSM_WGCNA_SRVC_DEA <- module_FA(miRSM_WGCNA_SRVC_genes, Analysis.type = 'DEA')
+}
+
+}
+\references{
+Zhang J, Liu L, Xu T, Xie Y, Zhao C, Li J, Le TD (2019). 
+“miRspongeR: an R/Bioconductor package for the identification and analysis of 
+miRNA sponge interaction networks and modules.” BMC Bioinformatics, 20, 235.
+
+Zhang J, Liu L, Zhang W, Li X, Zhao C, Li S, Li J, Le TD. 
+miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation. 
+Bioinform Adv. 2022 Sep 2;2(1):vbac063.
+
+Yu G, Wang L, Han Y, He Q (2012). 
+“clusterProfiler: an R package for comparing biological themes among gene clusters.” 
+OMICS: A Journal of Integrative Biology, 16(5), 284-287.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_GFA.Rd b/man/module_GFA.Rd
new file mode 100644
index 0000000..8e1816d
--- /dev/null
+++ b/man/module_GFA.Rd
@@ -0,0 +1,56 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_GFA}
+\alias{module_GFA}
+\title{module_GFA}
+\usage{
+module_GFA(
+  ceRExp,
+  mRExp = NULL,
+  StrengthCut = 0.9,
+  iter.max = 5000,
+  num.ModuleceRs = 2,
+  num.ModulemRs = 2
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{StrengthCut}{Desired minimum strength (absolute value of 
+association with interval [0 1]) for each bicluster.}
+
+\item{iter.max}{The total number of Gibbs sampling steps 
+(default 1000).}
+
+\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.}
+
+\item{num.ModulemRs}{The minimum number of mRNAs in each module.}
+}
+\value{
+GeneSetCollection object: a list of module genes.
+}
+\description{
+Identification of gene modules from matched ceRNA and mRNA 
+expression data using GFA package
+}
+\examples{
+data(BRCASampleData)
+modulegenes_GFA <- module_GFA(ceRExp[seq_len(20), seq_len(15)],
+    mRExp[seq_len(20), seq_len(15)], iter.max = 2600)
+
+}
+\references{
+Bunte K, Lepp\'{a}aho E, Saarinen I, Kaski S. 
+Sparse group factor analysis for biclustering of multiple data sources. Bioinformatics. 2016, 32(16):2457-63.
+
+Lepp\'{a}aho E, Ammad-ud-din M, Kaski S. GFA: 
+exploratory analysis of multiple data sources with group factor 
+analysis. J Mach Learn Res. 2017, 18(39):1-5.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_NMF.Rd b/man/module_NMF.Rd
new file mode 100644
index 0000000..5ba1eda
--- /dev/null
+++ b/man/module_NMF.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_NMF}
+\alias{module_NMF}
+\title{module_NMF}
+\usage{
+module_NMF(
+  ceRExp,
+  mRExp = NULL,
+  NMF.algorithm = "brunet",
+  num.modules = 10,
+  num.ModuleceRs = 2,
+  num.ModulemRs = 2
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{NMF.algorithm}{Specification of the NMF algorithm, 
+including 'brunet' (default), 'Frobenius', 'KL', 'lee', 'nsNMF', 
+'offset', 'siNMF', 'snmf/l', 'snmf/r'.}
+
+\item{num.modules}{The number of modules to be identified.}
+
+\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.}
+
+\item{num.ModulemRs}{The minimum number of mRNAs in each module.}
+}
+\value{
+GeneSetCollection object: a list of module genes.
+}
+\description{
+Identification of gene modules from matched ceRNA and mRNA 
+expression data using NMF package
+}
+\examples{
+data(BRCASampleData)
+# Reimport NMF package to avoid conflicts with DelayedArray package
+library(NMF)
+modulegenes_NMF <- module_NMF(ceRExp[, seq_len(10)],
+    mRExp[, seq_len(10)])
+
+}
+\references{
+Gaujoux R, Seoighe C. A flexible R package for 
+nonnegative matrix factorization. BMC Bioinformatics. 2010, 11:367.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_ProNet.Rd b/man/module_ProNet.Rd
new file mode 100644
index 0000000..c762b95
--- /dev/null
+++ b/man/module_ProNet.Rd
@@ -0,0 +1,71 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_ProNet}
+\alias{module_ProNet}
+\title{module_ProNet}
+\usage{
+module_ProNet(
+  ceRExp,
+  mRExp = NULL,
+  cor.method = "pearson",
+  pos.p.value.cutoff = 0.01,
+  cluster.method = "MCL",
+  num.ModuleceRs = 2,
+  num.ModulemRs = 2
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{cor.method}{The method of calculating correlation selected, 
+including 'pearson' (default), 'kendall', 'spearman'.}
+
+\item{pos.p.value.cutoff}{The significant p-value cutoff of 
+positive correlation}
+
+\item{cluster.method}{The clustering method selected in 
+\pkg{ProNet} package, including 'FN', 'MCL' (default), 
+'LINKCOMM', 'MCODE'.}
+
+\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.}
+
+\item{num.ModulemRs}{The minimum number of mRNAs in each module.}
+}
+\value{
+GeneSetCollection object: a list of module genes.
+}
+\description{
+Identification of gene modules from matched ceRNA and mRNA 
+expression data using ProNet package
+}
+\examples{
+data(BRCASampleData)
+modulegenes_ProNet <- module_ProNet(ceRExp[, seq_len(10)],
+    mRExp[, seq_len(10)])
+
+}
+\references{
+Clauset A, Newman ME, Moore C. Finding community 
+structure in very large networks. Phys Rev E Stat Nonlin Soft 
+Matter Phys., 2004, 70(6 Pt 2):066111.
+
+Enright AJ, Van Dongen S, Ouzounis CA. An efficient 
+algorithm for large-scale detection of protein families. 
+Nucleic Acids Res., 2002, 30(7):1575-84.
+
+Kalinka AT, Tomancak P. linkcomm: an R package 
+for the generation, visualization, and analysis of link 
+communities in networks of arbitrary size and type. 
+Bioinformatics, 2011, 27(14):2011-2.
+
+Bader GD, Hogue CW. An automated method for 
+finding molecular complexes in large protein interaction 
+networks. BMC Bioinformatics, 2003, 4:2.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_Validate.Rd b/man/module_Validate.Rd
new file mode 100644
index 0000000..c0dbaf7
--- /dev/null
+++ b/man/module_Validate.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_Validate}
+\alias{module_Validate}
+\title{module_Validate}
+\usage{
+module_Validate(Modulelist, Groundtruth)
+}
+\arguments{
+\item{Modulelist}{List object: a list of the identified miRNA sponge modules.}
+
+\item{Groundtruth}{Matrix object: a list of experimentally validated miRNA sponge interactions.}
+}
+\value{
+List object: a list of validated miRNA sponge interactions in each miRNA sponge module
+}
+\description{
+Validation of miRNA sponge interactions in each miRNA sponge module
+}
+\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]]
+Groundtruthcsv <- system.file("extdata", "Groundtruth.csv", package="miRSM")
+Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",") 
+miRSM.Validate <- module_Validate(miRSM_WGCNA_SRVC_genes, Groundtruth)
+
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_WGCNA.Rd b/man/module_WGCNA.Rd
new file mode 100644
index 0000000..23ff8bd
--- /dev/null
+++ b/man/module_WGCNA.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_WGCNA}
+\alias{module_WGCNA}
+\title{module_WGCNA}
+\usage{
+module_WGCNA(
+  ceRExp,
+  mRExp = NULL,
+  RsquaredCut = 0.9,
+  num.ModuleceRs = 2,
+  num.ModulemRs = 2
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{RsquaredCut}{Desired minimum scale free topology fitting index 
+R^2 with interval [0 1].}
+
+\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.}
+
+\item{num.ModulemRs}{The minimum number of mRNAs in each module.}
+}
+\value{
+GeneSetCollection object: a list of module genes.
+}
+\description{
+Identification of co-expressed gene modules from matched ceRNA and mRNA
+expression data using WGCNA package
+}
+\examples{
+data(BRCASampleData)
+modulegenes_WGCNA <- module_WGCNA(ceRExp[, seq_len(80)], 
+    mRExp[, seq_len(80)])
+
+}
+\references{
+Langfelder P, Horvath S. WGCNA: an R package for weighted 
+correlation network analysis. BMC Bioinformatics. 2008, 9:559.#'
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_biclust.Rd b/man/module_biclust.Rd
new file mode 100644
index 0000000..23defcf
--- /dev/null
+++ b/man/module_biclust.Rd
@@ -0,0 +1,112 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_biclust}
+\alias{module_biclust}
+\title{module_biclust}
+\usage{
+module_biclust(
+  ceRExp,
+  mRExp = NULL,
+  BCmethod = "fabia",
+  num.modules = 10,
+  num.ModuleceRs = 2,
+  num.ModulemRs = 2
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{BCmethod}{Specification of the biclustering method, 
+including 'BCBimax', 'BCCC', 'BCPlaid' (default), 'BCQuest', 
+'BCSpectral', 'BCXmotifs', iBBiG', 'fabia', 'fabiap', 
+'fabias', 'mfsc', 'nmfdiv', 'nmfeu', 'nmfsc', 'FLOC', 'isa', 
+'BCs4vd', 'BCssvd', 'bibit' and 'quBicluster'.}
+
+\item{num.modules}{The number of modules to be identified. For the 'BCPlaid',
+'BCSpectral', 'isa' and 'bibit' methods, no need to set the parameter. For the 
+'quBicluster' method, the parameter is used to set the number of biclusters 
+that should be reported.}
+
+\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.}
+
+\item{num.ModulemRs}{The minimum number of mRNAs in each module.}
+}
+\value{
+GeneSetCollection object: a list of module genes.
+}
+\description{
+Identification of gene modules from matched ceRNA and mRNA 
+expression data using a series of biclustering packages, 
+including biclust, iBBiG, fabia, BicARE, isa2, s4vd, 
+BiBitR and rqubic
+}
+\examples{
+data(BRCASampleData)
+modulegenes_biclust <- module_biclust(ceRExp[, seq_len(30)],
+    mRExp[, seq_len(30)])
+
+}
+\references{
+Preli\'{c} A, Bleuler S, Zimmermann P, Wille A, 
+B\'{u}hlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E. 
+A systematic comparison and evaluation of biclustering methods 
+for gene expression data. Bioinformatics. 2006, 22(9):1122-9.
+
+Cheng Y, Church GM. Biclustering of expression data. 
+Proc Int Conf Intell Syst Mol Biol. 2000, 8:93-103.
+
+Turner H, Bailey T, Krzanowski W. Improved 
+biclustering of microarray data demonstrated through systematic 
+performance tests. Comput Stat Data Anal. 2003, 48(2): 235-254.
+
+Murali TM, Kasif S. Extracting conserved gene 
+expression motifs from gene expression data. 
+Pac Symp Biocomput. 2003:77-88.
+
+Kluger Y, Basri R, Chang JT, Gerstein M. 
+Spectral biclustering of microarray data: coclustering genes 
+and conditions. Genome Res. 2003, 13(4):703-16.
+
+Gusenleitner D, Howe EA, Bentink S, Quackenbush J, 
+Culhane AC. iBBiG: iterative binary bi-clustering of gene sets. 
+Bioinformatics. 2012, 28(19):2484-92.
+
+Hochreiter S, Bodenhofer U, Heusel M, Mayr A, 
+Mitterecker A, Kasim A, Khamiakova T, Van Sanden S, Lin D, 
+Talloen W, Bijnens L, G\'{o}hlmann HW, Shkedy Z, Clevert DA. 
+FABIA: factor analysis for bicluster acquisition. 
+Bioinformatics. 2010, 26(12):1520-7.
+
+Yang J, Wang H, Wang W, Yu, PS. An improved 
+biclustering method for analyzing gene expression. 
+Int J Artif Intell Tools. 2005, 14(5): 771-789.
+
+Bergmann S, Ihmels J, Barkai N. Iterative 
+signature algorithm for the analysis of large-scale gene 
+expression data. Phys Rev E Stat Nonlin Soft Matter Phys. 
+2003, 67(3 Pt 1):031902.
+
+Sill M, Kaiser S, Benner A, Kopp-Schneider A. 
+Robust biclustering by sparse singular value decomposition 
+incorporating stability selection. Bioinformatics. 2011, 
+27(15):2089-97.
+
+Lee M, Shen H, Huang JZ, Marron JS. Biclustering 
+via sparse singular value decomposition. Biometrics. 2010, 
+66(4):1087-95.
+
+Rodriguez-Baena DS, Perez-Pulido AJ, Aguilar-Ruiz JS. 
+A biclustering algorithm for extracting bit-patterns from 
+binary datasets. Bioinformatics. 2011, 27(19):2738-45.
+
+Li G, Ma Q, Tang H, Paterson AH, Xu Y. 
+QUBIC: a qualitative biclustering algorithm for analyses of 
+gene expression data. Nucleic Acids Res. 2009, 37(15):e101.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_clust.Rd b/man/module_clust.Rd
new file mode 100644
index 0000000..2875caf
--- /dev/null
+++ b/man/module_clust.Rd
@@ -0,0 +1,106 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_clust}
+\alias{module_clust}
+\title{module_clust}
+\usage{
+module_clust(
+  ceRExp,
+  mRExp = NULL,
+  cluster.method = "kmeans",
+  num.modules = 10,
+  num.ModuleceRs = 2,
+  num.ModulemRs = 2
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{cluster.method}{Specification of the clustering method, 
+including 'kmeans'(default), 'hclust', 'dbscan' , 'clique', 
+'gmm', 'som' and 'fcm'.}
+
+\item{num.modules}{Parameter of the number of modules to be identified
+for the 'kmeans', 'hclust', 'gmm' and 'fcm' methods. Parameter of the number
+of intervals for the 'clique' method. For the 'dbscan' and 'som' methods,
+no need to set the parameter.}
+
+\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.}
+
+\item{num.ModulemRs}{The minimum number of mRNAs in each module.}
+}
+\value{
+GeneSetCollection object: a list of module genes.
+}
+\description{
+Identification of gene modules from matched ceRNA and mRNA 
+expression data using a series of clustering packages, 
+including stats, flashClust, dbscan, subspace, mclust, SOMbrero and ppclust packages.
+}
+\examples{
+data(BRCASampleData)
+modulegenes_clust <- module_clust(ceRExp[, seq_len(30)],
+    mRExp[, seq_len(30)])
+
+}
+\references{
+Forgy EW. Cluster analysis of multivariate 
+data: efficiency vs interpretability of classifications. 
+Biometrics, 1965, 21:768-769.
+
+Hartigan JA, Wong MA. 
+Algorithm AS 136: A K-means clustering algorithm. 
+Applied Statistics, 1979, 28:100-108.
+
+Lloyd SP. Least squares quantization in PCM. 
+Technical Note, Bell Laboratories. Published in 1982 
+in IEEE Transactions on Information Theory, 1982, 28:128-137.
+
+MacQueen J. Some methods for classification 
+and analysis of multivariate observations. 
+In Proceedings of the Fifth Berkeley Symposium on 
+Mathematical Statistics and Probability, 
+eds L. M. Le Cam & J. Neyman, 1967, 1, pp.281-297. 
+Berkeley, CA: University of California Press.
+
+Langfelder P, Horvath S. Fast R Functions for 
+Robust Correlations and Hierarchical Clustering. 
+Journal of Statistical Software. 2012, 46(11):1-17.
+
+Ester M, Kriegel HP, Sander J, Xu X. A density-based 
+algorithm for discovering clusters in large spatial databases with 
+noise, Proceedings of 2nd International Conference on Knowledge Discovery and
+Data Mining (KDD-96), 1996, 96(34): 226-231.
+
+Campello RJGB, Moulavi D, Sander J. 
+Density-based clustering based on hierarchical density estimates,
+Pacific-Asia conference on knowledge discovery and data mining. 
+Springer, Berlin, Heidelberg, 2013: 160-172.
+
+Agrawal R, Gehrke J, Gunopulos D, Raghavan P. 
+Automatic subspace clustering of high dimensional data for 
+data mining applications. In Proc. ACM SIGMOD, 1998.
+
+Scrucca L, Fop M, Murphy TB, Raftery AE. 
+mclust 5: clustering, classification and density estimation using 
+Gaussian finite mixture models The R Journal 8/1, 2016, pp. 205-233.
+
+Kohonen T. Self-Organizing Maps. 
+Berlin/Heidelberg: Springer-Verlag, 3rd edition, 2001.
+
+Dunn JC. A fuzzy relative of the ISODATA process 
+and its use in detecting compact well-separated clusters. Journal of Cybernetics, 
+1973, 3(3):32-57.
+
+Bezdek JC. Cluster validity with fuzzy sets. Journal of Cybernetics, 1974, 3: 58-73.
+
+Bezdek JC. Pattern recognition with fuzzy objective function 
+algorithms. Plenum, NY, 1981.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_group_sim.Rd b/man/module_group_sim.Rd
new file mode 100644
index 0000000..c988f19
--- /dev/null
+++ b/man/module_group_sim.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_group_sim}
+\alias{module_group_sim}
+\title{module_group_sim}
+\usage{
+module_group_sim(Module.group1, Module.group2, sim.method = "Simpson")
+}
+\arguments{
+\item{Module.group1}{List object, the first list of module group.}
+
+\item{Module.group2}{List object, the second list of module group.}
+
+\item{sim.method}{Methods for calculating similatiry between two modules, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.}
+}
+\value{
+Similarity between two list of module groups
+}
+\description{
+Calculating similarity between two list of module groups
+}
+\examples{
+library(GSEABase)
+data(BRCASampleData)
+modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp) 
+modulegenes_igraph <- module_igraph (ceRExp, mRExp) 
+Sim <- module_group_sim(geneIds(modulegenes_WGCNA), geneIds(modulegenes_igraph))
+
+}
+\references{
+Simpson E H. Measurement of diversity. Nature, 1949, 163(4148): 688-688.
+
+Jaccard P. The distribution of the flora in the alpine zone. 1. New phytologist, 1912, 11(2): 37-50.
+
+Lin D. An information-theoretic definition of similarity. in: Icml. 1998, 98(1998): 296-304.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_igraph.Rd b/man/module_igraph.Rd
new file mode 100644
index 0000000..949e2e2
--- /dev/null
+++ b/man/module_igraph.Rd
@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_igraph}
+\alias{module_igraph}
+\title{module_igraph}
+\usage{
+module_igraph(
+  ceRExp,
+  mRExp = NULL,
+  cor.method = "pearson",
+  pos.p.value.cutoff = 0.01,
+  cluster.method = "greedy",
+  num.ModuleceRs = 2,
+  num.ModulemRs = 2
+)
+}
+\arguments{
+\item{ceRExp}{A SummarizedExperiment object. ceRNA expression data: 
+rows are samples and columns are ceRNAs.}
+
+\item{mRExp}{NULL (default) or a SummarizedExperiment object. mRNA expression data: 
+rows are samples and columns are mRNAs.}
+
+\item{cor.method}{The method of calculating correlation selected, 
+including 'pearson' (default), 'kendall', 'spearman'.}
+
+\item{pos.p.value.cutoff}{The significant p-value cutoff of 
+positive correlation.}
+
+\item{cluster.method}{The clustering method selected in 
+\pkg{igraph} package, including 'betweenness', 'greedy' (default), 
+'infomap', 'prop', 'eigen', 'louvain', 'walktrap'.}
+
+\item{num.ModuleceRs}{The minimum number of ceRNAs in each module.}
+
+\item{num.ModulemRs}{The minimum number of mRNAs in each module.}
+}
+\value{
+GeneSetCollection object: a list of module genes.
+}
+\description{
+Identification of gene modules from matched ceRNA and mRNA 
+expression data using igraph package
+}
+\examples{
+data(BRCASampleData)
+modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)],
+    mRExp[, seq_len(10)])
+
+}
+\references{
+Csardi G, Nepusz T. The igraph software package for 
+complex network research, InterJournal, Complex Systems. 2006:1695.
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_miRdistribute.Rd b/man/module_miRdistribute.Rd
new file mode 100644
index 0000000..5dd275c
--- /dev/null
+++ b/man/module_miRdistribute.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_miRdistribute}
+\alias{module_miRdistribute}
+\title{module_miRdistribute}
+\usage{
+module_miRdistribute(share_miRs)
+}
+\arguments{
+\item{share_miRs}{List object: a list of common miRNAs of each miRNA sponge module 
+generated by share_miRs function.}
+}
+\value{
+Matrix object: miRNA distribution in each miRNA sponge module.
+}
+\description{
+miRNA distribution analysis of sharing miRNAs by the identified miRNA sponge modules
+}
+\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_share_miRs <-  share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes)
+miRSM_WGCNA_miRdistribute <- module_miRdistribute(miRSM_WGCNA_share_miRs)
+
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_miRsponge.Rd b/man/module_miRsponge.Rd
new file mode 100644
index 0000000..650f190
--- /dev/null
+++ b/man/module_miRsponge.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_miRsponge}
+\alias{module_miRsponge}
+\title{module_miRsponge}
+\usage{
+module_miRsponge(Modulelist)
+}
+\arguments{
+\item{Modulelist}{List object: a list of the identified miRNA sponge modules.}
+}
+\value{
+List object: miRNA sponge interactions of each miRNA sponge module.
+}
+\description{
+Extract miRNA sponge interactions of each miRNA sponge module
+}
+\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_miRsponge <- module_miRsponge(miRSM_WGCNA_SRVC_genes)
+
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/module_miRtarget.Rd b/man/module_miRtarget.Rd
new file mode 100644
index 0000000..3757cab
--- /dev/null
+++ b/man/module_miRtarget.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{module_miRtarget}
+\alias{module_miRtarget}
+\title{module_miRtarget}
+\usage{
+module_miRtarget(share_miRs, Modulelist)
+}
+\arguments{
+\item{share_miRs}{List object: a list of common miRNAs of each miRNA sponge module 
+generated by share_miRs function.}
+
+\item{Modulelist}{List object: a list of the identified miRNA sponge modules.}
+}
+\value{
+List object: miRNA-target interactions of each miRNA sponge module.
+}
+\description{
+Extract miRNA-target interactions of each miRNA sponge module
+}
+\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_share_miRs <-  share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes)
+miRSM_WGCNA_miRtarget <- module_miRtarget(miRSM_WGCNA_share_miRs, 
+                                          miRSM_WGCNA_SRVC_genes)
+
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}
diff --git a/man/share_miRs.Rd b/man/share_miRs.Rd
new file mode 100644
index 0000000..3420d89
--- /dev/null
+++ b/man/share_miRs.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/miRSM.R
+\name{share_miRs}
+\alias{share_miRs}
+\title{share_miRs}
+\usage{
+share_miRs(miRTarget, Modulelist)
+}
+\arguments{
+\item{miRTarget}{A SummarizedExperiment object. Putative 
+miRNA-target binding information.}
+
+\item{Modulelist}{List object: a list of the identified miRNA sponge modules.}
+}
+\value{
+List object: a list of common miRNAs of each miRNA sponge module.
+}
+\description{
+Extract common miRNAs of each miRNA sponge module
+}
+\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_share_miRs <-  share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes)
+
+}
+\author{
+Junpeng Zhang (\url{https://www.researchgate.net/profile/Junpeng-Zhang-2})
+}