miRLAB (version 1.2.2)

Pearson: miRNA target prediction with the Pearson correlation coefficient method

Description

Calculate the Pearson correlation coefficient of each pair of miRNA-mRNA,and return a matrix of correlation coefficients with columns are miRNAs and rows are mRNAs.

Usage

Pearson(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 Pearson correlation coefficients. Columns are miRNAs, rows are mRNAs.

References

Pearson, K. (1920) Notes on the history of correlation. Biometrika, 13, 25 - 45.

Examples

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