TPEA: A Novel Topology-Based Pathway Enrichment Analysis Approach

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.

AuthorWei Jiang
Date of publication2017-01-03 07:33:51
MaintainerWei Jiang <jiangwei@hrbmu.edu.cn>
LicenseGPL-2
Version3.0

View on CRAN

Man pages

all_genes: All human protein coding genes

AUCSC: Calculate the area under the cumulative enrichment 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 from KEGG database.

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...

Functions

all_genes Man page
AUEC Man page
DownloadKGML Man page
filterNode Man page
gene2ec Man page
gene2ko Man page
getEntry Man page
getGeneFromEnzyme Man page
getGeneFromKGene Man page
getGeneFromKO Man page
getGraphics Man page
getKGeneFromEnzyme Man page
getKGeneFromKO Man page
getNonMetabolicGraph Man page
getOrgAndIdType Man page
getPathway Man page
getProduct Man page
getReaction Man page
getRelation Man page
getSimpleGraph Man page
getSubstrate Man page
getSubtype Man page
getUGraph Man page
getUnknowProduct Man page
getUnknowReaction Man page
getUnknowRelation Man page
getUnknowSubstrate Man page
getUnknowSubtype Man page
importLatesData Man page
keggGene2gene Man page
mapNode Man page
node_gene Man page
NodeGene Man page
NodeGeneData Man page
num_node_gene_score Man page
PathNetwork Man page
pathway_names Man page
simplifyGraph Man page
TPEA Man page
TPEA-package Man page
UPDATE Man page
ViewLatestTime Man page
viewpathway Man page

Files

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/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/AUEC.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

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