## ----style, echo=FALSE, results="asis", message=FALSE------------------------- BiocStyle::markdown() knitr::opts_chunk$set(tidy = FALSE, warning = FALSE, message = FALSE) ## ----echo=FALSE, results='hide', message=FALSE-------------------------------- library(miRspongeR) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology") head(miRHomologyceRInt) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR") ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE) pcceRInt <- spongeMethod(miRTarget, ExpData, method = "pc") head(pcceRInt) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR") ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE) sppcceRInt <- spongeMethod(miRTarget, ExpData, senscorcutoff = 0.1, method = "sppc") head(sppcceRInt) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR") ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE) hermesceRInt <- spongeMethod(miRTarget, ExpData, num_perm = 10, method = "hermes") head(hermesceRInt) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR") ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE) ppcceRInt <- spongeMethod(miRTarget, ExpData, num_perm = 10, method = "ppc") head(ppcceRInt) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") MREs <- system.file("extdata", "MREs.csv", package="miRspongeR") mres <- read.csv(MREs, header=TRUE, sep=",") muTaMEceRInt <- spongeMethod(miRTarget, mres = mres, method = "muTaME") head(muTaMEceRInt) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") MREs <- system.file("extdata", "MREs.csv", package="miRspongeR") mres <- read.csv(MREs, header=TRUE, sep=",") ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR") ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE) cerniaceRInt <- spongeMethod(miRTarget, ExpData, mres, method = "cernia") head(cerniaceRInt) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR") ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE) miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology") pcceRInt <- spongeMethod(miRTarget, ExpData, method = "pc") sppcceRInt <- spongeMethod(miRTarget, ExpData, method = "sppc") Interlist <- list(miRHomologyceRInt[, 1:2], pcceRInt[, 1:2], sppcceRInt[, 1:2]) IntegrateceRInt <- integrateMethod(Interlist, Intersect_num = 2) head(IntegrateceRInt) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology") Groundtruthcsv <- system.file("extdata", "Groundtruth.csv", package="miRspongeR") Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",") spongenetwork_validated <- spongeValidate(miRHomologyceRInt[, 1:2], directed = FALSE, Groundtruth) spongenetwork_validated ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology") spongenetwork_Cluster <- netModule(miRHomologyceRInt[, 1:2], modulesize = 2) spongenetwork_Cluster ## ---- eval=FALSE, include=TRUE------------------------------------------------ # miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") # miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") # miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology") # spongenetwork_Cluster <- netModule(miRHomologyceRInt[, 1:2], modulesize = 2) # sponge_Module_DEA <- moduleDEA(spongenetwork_Cluster) # sponge_Module_FEA <- moduleFEA(spongenetwork_Cluster) ## ----------------------------------------------------------------------------- miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR") miRTarget <- read.csv(miR2Target, header=TRUE, sep=",") ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR") ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE) SurvDatacsv <- system.file("extdata", "SurvData.csv", package="miRspongeR") SurvData <- read.csv(SurvDatacsv, header=TRUE, sep=",") pcceRInt <- spongeMethod(miRTarget, ExpData, method = "pc") spongenetwork_Cluster <- netModule(pcceRInt[, 1:2], modulesize = 2) sponge_Module_Survival <- moduleSurvival(spongenetwork_Cluster, ExpData, SurvData, devidePercentage=.5) sponge_Module_Survival ## ----------------------------------------------------------------------------- sessionInfo()