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Last data update: 2014.03.03

R: Get the co-express lncRNA-mRNA interactions

getLncGenePairs

R Documentation

Get the co-express lncRNA-mRNA interactions

Description

Get the co-express lncRNA-mRNA interactions reached a significant positive threshold. These lncRNAs-mRNAs pairs are competitivly rugulated.

Usage

getLncGenePairs(GeneExp,LncExp,a=0.025)

Arguments

`GeneExp`	A gene expression profile. The first row of gene expression profile is names of mRNA, and the gene expression profile and the lncRNA expression profile must be mached.
`LncExp`	A lncRNA expression profile. The first row of lncRNA expression profile is names of lncRNA, and the gene expression profile and the lncRNA expression profile must be mached.
`a`	A parameter,namely the significant positive threshold.

Details

Co-express coefficient for any pair of relations in the candidate LncRNA-mRNA network is calculated basing on matched LncRNA and mRNA expression profiles, those relations had reached a significant positive threshold were retained.

Value

A data frame. The data frame has two columns, the fist is lncRNA names, the other is mRNA names.

Author(s)

Xinrui Shi, Chunquan Li and Xia Li

Examples

## Not run: 


 GeneExp<-GetExampleData(exampleData="GeneExp")
 LncExp<-GetExampleData(exampleData="LncExp")
 LncGenePairs<-getLncGenePairs(GeneExp,LncExp,a=0.025)
 
## End(Not run)