
identifyGraph(moleculeList,graphList,type="gene_miRNA", background=getBackground(type), order="pvalue",decreasing=FALSE)
list
can be converted to the data.frame
by the function printGraph
.Note that moleculeList
must be a 'character' vector. The genes must be represented by NCBI gene ids, and miRNAs must be represented by mature miRNA name in miRBase.
The function can support the annotation and identification of metabolic subpathways based on genes, miRNAs or gene_miRNAs sets. The argument moleculeList
supports three kinds of molecular sets: "genes", "miRNAs" or "gene_miRNAs".
The argument type
represent the type of input molecules, including one of "genes", "miRNAs" or "gene_miRNA".
Detailed background
information is provided in the function getBackground
.
When many correlated subpathways are considered, the parameter order
is used to order the pathways on the basis of "pvalue" or "fdr".
The parameter decreasing
is set TRUE that represent the order would be performed by decreasing.
printGraph
, getBackground
, GetK2riData
## Not run:
#
# ### Annotate and identify subpathways ###
#
# ## 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 user-interested miRNAs and genes sets.
# moleculeList <- c(getBackground(type="gene")[1:1000],
# getBackground(type="miRNA")[1:2000])
#
#
# ## get direct KEGG metabolic pathway graphs ##
# graphList <- GetK2riData(K2riData="MetabolicGEGEEMGraph")
# # get reconstructed pathway graph list.
# InteGraphList <- getInteGraphList(graphList, relations)
# # 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)
#
# ## get undirect KEGG metabolic pathway graphs ##
# graphList <- GetK2riData(K2riData="MetabolicGEGEUEMGraph")
# # get reconstructed pathway graph list.
# InteGraphList <- getInteGraphList(graphList, relations)
# # 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")
# 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)
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