getInteGraphList: Get the reconstructed metabolic pathway graphs

Description Usage Arguments Details Value Author(s) See Also Examples

Description

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

Usage

1
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

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## 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)


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