getLncGenePairs: Get the co-express lncRNA-mRNA interactions

In SubpathwayLNCE: Identify Signal Subpathways Competitively Regulated by LncRNAs Based on ceRNA Theory

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)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:igraph':

    normalize, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'graph'

The following objects are masked from 'package:igraph':

    degree, edges, intersection


Attaching package: 'RBGL'

The following objects are masked from 'package:igraph':

    bfs, dfs, transitivity

Loading required package: BiasedUrn

Attaching package: 'SubpathwayLNCE'

The following object is masked from 'package:graph':

    initialize

The following object is masked from 'package:methods':

    initialize

SubpathwayLNCE documentation built on May 1, 2019, 10:25 p.m.