miRLAB (version 1.2.2)

Spearman: miRNA target prediction with the Spearman correlation coefficient method

Description

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

Usage

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

References

Spearman, C. (1904) General intelligence, objectively determined and measured. Am. J. Psychol., 15, 201 - 92.

Examples

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