miRLAB (version 1.2.2)

ProMISe: miRNA target prediction with the ProMISe method

Description

Calculate the ProMISe score of each pair of miRNA-mRNA, and return a matrix of values with columns are miRNAs and rows are mRNAs.

Usage

ProMISe(datacsv, cause, effect, targetbinding = NA)

Arguments

datacsv
the input dataset in csv format
cause
the column range that specifies the causes (miRNAs), e.g. 1:35
effect
the column range that specifies the effects (mRNAs), e.g. 36:2000
targetbinding
the putative target, e.g. "TargetScan.csv". If targetbinding is not specified, only expression data is used. If targetbinding is specified, the prediction results using expression data with be intersected with the interactions in the target binding file.

Value

  • A matrix that includes the ProMISe scores. Columns are miRNAs, rows are mRNAs.

References

Li, Y., Liang, C., Wong, K.C., Jin, K., and Zhang, Z. (2014). Inferring probabilistic miRNA - mRNA interaction signatures in cancers: a role-switch approach. Nucleic Acids Res., 42, e76-e76.

Examples

dataset=system.file("extdata", "ToyEMT.csv", package="miRLAB")
results=ProMISe(dataset, 1:3, 4:18)