spongeValidate: Validation of computationally predicted miRNA sponge...

In zhangjunpeng411/miRspongeR: Identification and analysis of miRNA sponge regulation

Validation of computationally predicted miRNA sponge interactions

Description

Validation of computationally predicted miRNA sponge interactions. The built-in groundtruth of miRNA sponge interactions are from miRSponge (<http://bio-bigdata.hrbmu.edu.cn/miRSponge/>), lncACTdb (<http://bio-bigdata.hrbmu.edu.cn/LncACTdb/>), LncCeRBase (<http://www.insect-genome.com/LncCeRBase/front/>).

Usage

spongeValidate(spongenetwork, directed = FALSE, Groundtruth)

Arguments

spongenetwork	Input miRNA sponge interaction network.
directed	A logical value, the network is directed or not.
Groundtruth	The groundtruth of miRNA sponge interactions.

Value

A list of experimentally validated miRNA sponge interactions.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)

Examples

# Obtain miRNA-target interaction data file "miR2Target.csv" in csv format
miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR")
miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")

# Obtain experimentally validated miRNA sponge interaction data file "Groundtruth.csv" in csv format
Groundtruthcsv <- system.file("extdata", "Groundtruth.csv", package="miRspongeR")
Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",")
miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology")
spongenetwork_validated <- spongeValidate(miRHomologyceRInt[, 1:2], directed = FALSE, Groundtruth)

zhangjunpeng411/miRspongeR documentation built on Sept. 28, 2022, 2:34 p.m.