MI: miRNA target prediction with mutual information method
Description
Calculate the mutual information of each pair of miRNA-mRNA,and return a matrix of mutual information values with columns are miRNAs and rows are mRNAs.
Usage
MI(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 mutual information values. Columns are miRNAs, rows are mRNAs.
References
Moon, Y.I., Balaji, R., and Lall, U. (1995) Estimation of mutual information using kernel density estimators. Phys. Rev. E, 52, 2318 - 21.