# miRSM R package
# Introduction
This package provides several functions to study miRNA sponge modules.
# Installation
```{r echo=FALSE, results='hide', message=FALSE}
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("miRSM")
```
# A quick example to use miRSM package
```{r echo=FALSE, results='hide', message=FALSE}
# Load miRSM package
suppressMessages(library(miRSM))
# Load BRCA sample data
data(BRCASampleData)
# Identify ceRNA-mRNA co-expression modules using WGCNA
modulegenes_WGCNA <- module_WGCNA(ceRExp[, seq_len(150)],
mRExp[, seq_len(150)])
# 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")
# Functional analysis of miRNA sponge modules
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")
# Cancer enrichment analysis of miRNA sponge modules
miRSM.CEA.pvalue <- module_CEA(ceRExp, mRExp, BRCA_genes, miRSM_WGCNA_SRVC_genes)
# Validation of miRNA sponge interactions in miRNA sponge modules
library(miRspongeR)
Groundtruthcsv <- system.file("extdata", "Groundtruth.csv", package="miRspongeR")
Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",")
miRSM.Validate <- module_Validate(miRSM_WGCNA_SRVC_genes, Groundtruth)
# Co-expression analysis of miRNA sponge modules
miRSM_WGCNA_Coexpress <- module_Coexpress(ceRExp, mRExp, miRSM_WGCNA_SRVC_genes, resample = 10, method = "mean", test.method = "t.test")
# miRNA distribution analysis of sharing miRNAs
miRSM_WGCNA_share_miRs <- share_miRs(miRExp, ceRExp, mRExp, miRTarget, miRSM_WGCNA_SRVC_genes)
miRSM_WGCNA_miRdistribute <- module_miRdistribute(miRSM_WGCNA_share_miRs)
# Predict miRNA-target interactions
miRSM_WGCNA_miRtarget <- module_miRtarget(miRSM_WGCNA_share_miRs, miRSM_WGCNA_SRVC_genes)
# Identify miRNA sponge interactions
miRSM_WGCNA_miRsponge <- module_miRsponge(ceRExp, mRExp, miRSM_WGCNA_SRVC_genes)
```
# License
GPL-3
