SubpathwayGMir (version 1.0)

printGraph: Print the results of graph annotation and identification

Description

Print the results of graph annotation and identification.

Usage

printGraph(ann,detail=FALSE)

Arguments

ann

A list. The value was returned from the function identifyGraph.

detail

A logical. If true, gene lists from the function identifyGraph are converted into strings, which are used to display and write results with genes.

Value

A data.frame. Columns include pathwayId, pathwayName, annMoleculeRatio, annBgRatio, pvalue, 'fdr', annMoleculeList, annBgMoleculeList. Detailed information is provided in identifyGraph.

See Also

identifyGraph

Examples

## Not run: 
# 
# # 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) 
# 
# # get user-interested miRNAs and genes sets.
#  moleculeList <- c(getBackground(type="gene")[1:1000],
#                   getBackground(type="miRNA")[1:2000])
# 				  
# # get locate subpathways.
#  subGraphList <- getLocSubGraph(moleculeList,InteGraphList,
#                  type="gene_miRNA",n=1,s=10)
# 				 
# # annotate and identify subpathways.
#  ann <- identifyGraph(moleculeList,subGraphList,type="gene_miRNA")
# 
# # convert ann to a data frame.
#  result <- printGraph(ann,detail=TRUE)
# 
# # save the result.
#  write.table(head(result),"result.txt",sep="\t",col.names=TRUE,row.names=FALSE)
# 
# ## End(Not run)