miRLAB (version 1.2.2)

Validation: Validate the targets of a miRNA

Description

Given the predicted target of a miRNA, the function returns a list of targets that are experimentally confirmed based on the provided ground truth. Users can provide their own ground truth or use the built-in ground truth which is the union of Tarbase, miRTarbase, miRecords, and miRWalk.

Usage

Validation(topkList, datacsv)

Arguments

topkList

a matrix with 3 columns. The first column is the miRNA name, the second contains the target mRNAs, and the third contains the correlation values/ causal effects/ scores

datacsv

the ground truth for the validation. The ground truth is a matrix with 2 columns, where the first column is the miRNA and the second is the mRNA.

Value

• a matrix in the same format of the input matrix put only contains the confirmed interactions.

Examples

dataset=system.file("extdata", "ToyEMT.csv", package="miRLAB")
ps=Pearson(dataset, cause=1:3, effect=4:18)
miR200aTop10=bRank(ps, 3, 10, TRUE)
groundtruth=system.file("extdata", "Toygroundtruth.csv", package="miRLAB")
miR200aTop10Confirmed = Validation(miR200aTop10, groundtruth)