getInteGraphList: Get the reconstructed metabolic pathway graphs

In SubpathwayGMir: Identify Metabolic Subpathways Mediated by MicroRNAs

Description

Get the reconstructed KEGG metabolic pathway graphs embedded by miRNAs through integrating experimentally verified miRNA-target interactions.

Usage

getInteGraphList(graphList,relations)

Arguments

graphList	A graphList. There nodes must be represented by genes.
relations	A data frame. It contains two columns, the first is miRNA names and the second is its target names.

Details

The argument "relations" represents user-interested miRNA-target interactions, which can be returned from the GetK2riData.

Value

A graph list.

Author(s)

Li Feng, Chunquan Li and Xia Li

See Also

plotGraph, getLocSubGraph, GetK2riData

Examples

## Not run: 

### Integrate miRNAs into KEGG pathway graphs ###

## get hsa-specificd miRNA-target interactions ##
 expMir2Tar <- GetK2riData(K2riData="expMir2Tar")
 row1 <- which(expMir2Tar[["LowTHExps"]]=="YES")
 row2 <- which(expMir2Tar[["Species"]]=="hsa")
 relations <- unique(expMir2Tar[intersect(row1,row2),c(2:3)])

## get direct KEGG metabolic pathway graphs ## 
 graphList <- GetK2riData(K2riData="MetabolicGEGEEMGraph")
# get reconstructed pathway graph list #
 InteGraphList <- getInteGraphList(graphList, relations) 
# visualize the reconstructed pathways #
 plotGraph(InteGraphList[[1]],layout=layout.random)

## get undirect KEGG metabolic pathway graphs ##
 graphList <- GetK2riData(K2riData="MetabolicGEGEUEMGraph")
# get reconstructed pathway graph list #
 InteGraphList <- getInteGraphList(graphList, relations) 
# visualize the reconstructed pathways #
 plotGraph(InteGraphList[[1]],layout=layout.random)
 
## End(Not run)

SubpathwayGMir documentation built on May 2, 2019, 2:39 a.m.