gene.trait.similarity {BUS} | R Documentation

## Calculate similarity for gene-trait interaction

### Description

To calculate similarity for gene-trait interaction (using correlation/mutual information metric).

### Usage

    gene.trait.similarity(EXP, trait, measure, na.replica = 50)

### Arguments

`EXP` | Gene expression data in form of a matrix. Row stands for genes and column for experiments.
`trait` | Trait data in form of matrix. Row stands for traits and column for experiments.
`measure` | Metric used to calculate similarity: "corr" for correlation, "MI" for mutual information.
`na.replica` | Times of replicates for filling NANs in impute method; default value is 50. The (smooth) bootstrapping approach is used to give an estimation to missing value in the data.

### Value

A matrix, row stands for gene and column for trait. Element in row i and column j stands for the association between the gene i and trait j.

### Author(s)

Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini

### Examples

    data(tumors.mRNA)
    data(tumors.miRNA)
    exp<-tumors.mRNA
    trait<-tumors.miRNA
    gene.trait.similarity(EXP= exp[1:10, ],trait= trait[1:5, ],measure="MI")

[Package BUS version 1.40.0 Index]