miRSM - miRSM 2.0.0

miRSM R package

Introduction

This package provides several utility functions to study miRNA sponge or ceRNA modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of 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)

Identifying gene co-expression modules using WGCNA

modulegenesWGCNA <- moduleWGCNA(ceRExp[, seqlen(150)], mRExp[, seqlen(150)])

Identifying miRNA sponge modules using sensitivity RV coefficient (SRVC)

miRSMWGCNASRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, modulegenesWGCNA, method = "SRVC", SMC.cutoff = 0.01, RVmethod = "RV")

Identifying sample-specific miRNA sponge modules

nsamples <- 3 modulegenesigraphall <- moduleigraph(ceRExp[, 151:300], mRExp[, 151:300]) modulegenesWGCNAexceptk <- lapply(seq(nsamples), function(i) moduleWGCNA(ceRExp[-i, seq(150)], mRExp[-i, seq(150)])) miRSMigraphSRVCall <- miRSM(miRExp, ceRExp[, 151:300], mRExp[, 151:300], miRTarget, modulegenesigraphall, method = "SRVC", SMC.cutoff = 0.01, RVmethod = "RV") miRSMWGCNASRVCexceptk <- lapply(seq(nsamples), function(i) miRSM(miRExp[-i, ], ceRExp[-i, seq(150)], mRExp[-i, seq(150)], miRTarget, modulegenesWGCNAexceptk[[i]], method = "SRVC", SMC.cutoff = 0.01, RVmethod = "RV")) Modulegenesall <- miRSMigraphSRVCall[[2]] Modulegenesexceptk <- lapply(seq(nsamples), function(i) miRSMWGCNASRVCexceptk[[i]][[2]]) ModulesSS <- miRSMSS(Modulegenesall, Modulegenesexceptk)

Functional analysis of miRNA sponge modules

miRSMWGCNASRVCgenes <- miRSMWGCNASRVC[[2]] miRSMWGCNASRVCFEA <- moduleFA(miRSMWGCNASRVCgenes, Analysis.type ="FEA") miRSMWGCNASRVCDEA <- moduleFA(miRSMWGCNASRVC_genes, Analysis.type = "DEA")

Cancer enrichment analysis of miRNA sponge modules

miRSM.CEA.pvalue <- moduleCEA(ceRExp, mRExp, BRCAgenes, miRSMWGCNASRVC_genes)

Validation of miRNA sponge interactions in miRNA sponge modules

Groundtruthcsv <- system.file("extdata", "Groundtruth.csv", package="miRSM") Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",") miRSM.Validate <- moduleValidate(miRSMWGCNASRVCgenes, Groundtruth)

Co-expression analysis of miRNA sponge modules

miRSMWGCNACoexpress <- moduleCoexpress(ceRExp, mRExp, miRSMWGCNASRVCgenes, resample = 10, method = "mean", test.method = "t.test")

Distribution analysis of sharing miRNAs

miRSMWGCNAsharemiRs <- sharemiRs(miRTarget, miRSMWGCNASRVCgenes) miRSMWGCNAmiRdistribute <- modulemiRdistribute(miRSMWGCNAshare_miRs)

Predicting miRNA-target interactions

miRSMWGCNAmiRtarget <- modulemiRtarget(miRSMWGCNAsharemiRs, miRSMWGCNASRVC_genes)

Identifying miRNA sponge interactions

miRSMWGCNAmiRsponge <- modulemiRsponge(miRSMWGCNASRVCgenes)

```

License

GPL-3

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Published by zhangjunpeng411 over 1 year ago