spongeValidate {miRsponge} | R Documentation |
Validation of computationally predicted miRNA sponge interactions. The groundtruth of miRNA sponge interactions are from miRSponge (http://www.bio-bigdata.net/miRSponge/) and the experimentally validated miRNA sponge interactions of related literatures.
spongeValidate(spongenetwork, directed = FALSE, Groundtruth)
spongenetwork |
Input miRNA sponge interaction network. |
directed |
A logical value, the network is directed or not. |
Groundtruth |
The groundtruth of miRNA sponge interactions. |
A list of experimentally validated miRNA sponge interactions.
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
# Obtain miRNA-target interaction data file "miR2Target.csv" in csv format miR2Target <- system.file("extdata", "miR2Target.csv", package="miRsponge") 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="miRsponge") Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",") miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology") spongenetwork_validated <- spongeValidate(miRHomologyceRInt[, 1:2], directed = FALSE, Groundtruth)