Validation: Validate the targets of a miRNA
In miRLAB: Dry lab for exploring miRNA-mRNA relationships
Description
Usage
Arguments
Value
Examples
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
1
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
1
2
3
4
5
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)
miRLAB documentation built on Nov. 8, 2020, 5:45 p.m.
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Description Usage Arguments Value Examples
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
1 | 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
1 2 3 4 5 | 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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