SubpathwayGMir (version 1.0)

getInteGraphList: Get the reconstructed metabolic pathway graphs

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.

Value

A graph list.

Details

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

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)