R: Print the results of graph annotation and identification
printGraph
R Documentation
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.
Author(s)
Li Feng, Chunquan Li and Xia Li
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)