TPEA: A Novel Topology-Based Pathway Enrichment Analysis Approach

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We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database. We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.

Author
Wei Jiang
Date of publication
2016-10-26 10:37:45
Maintainer
Wei Jiang <jiangwei@hrbmu.edu.cn>
License
GPL-2
Version
2.0

View on CRAN

Man pages

all_genes
All human protein coding genes
AUCSC
Calculate the area under the cumulative score of node curve...
DownloadKGML
Download the latest KGML files
filterNode
Filter the nodes in pathways
gene2ec
The relationship of genes and EC
gene2ko
The relationship of genes and KO
getEntry
Obtain the nodes
getGeneFromEnzyme
Obtain the genes from enzymes
getGeneFromKGene
Obtain the genes from KGenes
getGeneFromKO
Obtain the genes from KO
getGraphics
Recontructe the network based on pathways
getKGeneFromEnzyme
Obtain genes from KGnenes
getKGeneFromKO
Obtain the genes from KO
getNonMetabolicGraph
Convert the non-metaboloc pathway to network
getOrgAndIdType
Get the type names of nodes
getPathway
Get the pathway
getProduct
Get the products
getReaction
Get the reaction of nodes in pathways
getRelation
Get the relation of nodes in pathways
getSimpleGraph
Obtain the graph of pathways
getSubstrate
Obtain the information about nodes in KEGG database
getSubtype
Get the type of nodes
getUGraph
Obtain the graph of pathways
getUnknowProduct
Get the products
getUnknowReaction
Get the reaction of nodes in pathways
getUnknowRelation
Get the relation of nodes in pathways
getUnknowSubstrate
Obtain the information about nodes in KEGG database
getUnknowSubtype
Obtain the types of genes in pathways
importLatesData
Import the latest relationship information.
keggGene2gene
KeggGene to genes
mapNode
Obtain the relationship of nodes and genes
node_gene
The relationship between nodes and genes
NodeGene
Restract the relationship between nodes and genes.
NodeGeneData
Intergate list of node,gene and the score of node.
num_node_gene_score
The score of each node in a certain pathway
PathNetwork
Reconstruct pathways to networks
pathway_names
Pathway names in KEGG Database
simplifyGraph
Recontructe the network based on pathways
TPEA
Statistical test and calculate the significance
TPEA-package
TPEA: A novel topology-based pathway enrichment analysis...
UPDATE
Update the latest data from KEGG database
ViewLatestTime
Check up the latest date of KGML files
viewpathway
The visualization of interested pathway based on the genes...

Files in this package

TPEA
TPEA/NAMESPACE
TPEA/data
TPEA/data/pathway_names.rda
TPEA/data/keggGene2gene.rda
TPEA/data/gene2ko.rda
TPEA/data/all_genes.rda
TPEA/data/node_gene.rda
TPEA/data/gene2ec.rda
TPEA/data/num_node_gene_score.rda
TPEA/R
TPEA/R/filterNode.R
TPEA/R/getPathway.R
TPEA/R/getNonMetabolicGraph.R
TPEA/R/getUnknowSubstrate.R
TPEA/R/getSimpleGraph.R
TPEA/R/importLatesData.R
TPEA/R/PathNetwork.R
TPEA/R/AUCSC.R
TPEA/R/getProduct.R
TPEA/R/UPDATE.R
TPEA/R/getGeneFromEnzyme.R
TPEA/R/getGeneFromKO.R
TPEA/R/getUGraph.R
TPEA/R/simplifyGraph.R
TPEA/R/getSubtype.R
TPEA/R/TPEA.R
TPEA/R/NodeGene.R
TPEA/R/NodeGeneData.R
TPEA/R/getKGeneFromEnzyme.R
TPEA/R/getReaction.R
TPEA/R/ViewLatestTime.R
TPEA/R/getKGeneFromKO.R
TPEA/R/getEntry.R
TPEA/R/getUnknowProduct.R
TPEA/R/getUnknowRelation.R
TPEA/R/getOrgAndIdType.R
TPEA/R/viewpathway.R
TPEA/R/DownloadKGML.R
TPEA/R/getGeneFromKGene.R
TPEA/R/getRelation.R
TPEA/R/getUnknowSubtype.R
TPEA/R/getUnknowReaction.R
TPEA/R/mapNode.R
TPEA/R/getGraphics.R
TPEA/R/getSubstrate.R
TPEA/MD5
TPEA/DESCRIPTION
TPEA/man
TPEA/man/getEntry.Rd
TPEA/man/getPathway.Rd
TPEA/man/getUGraph.Rd
TPEA/man/all_genes.Rd
TPEA/man/getUnknowReaction.Rd
TPEA/man/NodeGeneData.Rd
TPEA/man/ViewLatestTime.Rd
TPEA/man/getSubtype.Rd
TPEA/man/simplifyGraph.Rd
TPEA/man/getProduct.Rd
TPEA/man/AUCSC.Rd
TPEA/man/getUnknowSubstrate.Rd
TPEA/man/getSubstrate.Rd
TPEA/man/getOrgAndIdType.Rd
TPEA/man/node_gene.Rd
TPEA/man/gene2ec.Rd
TPEA/man/num_node_gene_score.Rd
TPEA/man/getUnknowSubtype.Rd
TPEA/man/getUnknowRelation.Rd
TPEA/man/getUnknowProduct.Rd
TPEA/man/UPDATE.Rd
TPEA/man/TPEA.Rd
TPEA/man/DownloadKGML.Rd
TPEA/man/getNonMetabolicGraph.Rd
TPEA/man/getRelation.Rd
TPEA/man/TPEA-package.Rd
TPEA/man/gene2ko.Rd
TPEA/man/pathway_names.Rd
TPEA/man/viewpathway.Rd
TPEA/man/filterNode.Rd
TPEA/man/keggGene2gene.Rd
TPEA/man/getReaction.Rd
TPEA/man/getKGeneFromKO.Rd
TPEA/man/getSimpleGraph.Rd
TPEA/man/mapNode.Rd
TPEA/man/getGeneFromKGene.Rd
TPEA/man/getKGeneFromEnzyme.Rd
TPEA/man/NodeGene.Rd
TPEA/man/getGraphics.Rd
TPEA/man/getGeneFromEnzyme.Rd
TPEA/man/importLatesData.Rd
TPEA/man/PathNetwork.Rd
TPEA/man/getGeneFromKO.Rd
TPEA/INDEX