TPEA: A Novel Topology-Based Pathway Enrichment Analysis Approach
Version 3.0

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TPEA")

Getting started

Package overview

Popular man pages

AUCSC: Calculate the area under the cumulative enrichment curve...
getGeneFromKGene: Obtain the genes from KGenes
getOrgAndIdType: Get the type names of nodes
getUnknowProduct: Get the products
NodeGene: Restract the relationship between nodes and genes.
pathway_names: Pathway names in KEGG Database
simplifyGraph: Recontructe the network based on pathways
See all...

All man pages Function index File listing

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

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

Files

NAMESPACE
data
data/pathway_names.rda
data/keggGene2gene.rda
data/gene2ko.rda
data/all_genes.rda
data/node_gene.rda
data/gene2ec.rda
data/num_node_gene_score.rda
R
R/filterNode.R
R/getPathway.R
R/getNonMetabolicGraph.R
R/getUnknowSubstrate.R
R/getSimpleGraph.R
R/importLatesData.R
R/PathNetwork.R
R/getProduct.R
R/UPDATE.R
R/getGeneFromEnzyme.R
R/getGeneFromKO.R
R/getUGraph.R
R/simplifyGraph.R
R/getSubtype.R
R/TPEA.R
R/NodeGene.R
R/NodeGeneData.R
R/getKGeneFromEnzyme.R
R/getReaction.R
R/ViewLatestTime.R
R/getKGeneFromKO.R
R/getEntry.R
R/getUnknowProduct.R
R/getUnknowRelation.R
R/getOrgAndIdType.R
R/viewpathway.R
R/DownloadKGML.R
R/AUEC.R
R/getGeneFromKGene.R
R/getRelation.R
R/getUnknowSubtype.R
R/getUnknowReaction.R
R/mapNode.R
R/getGraphics.R
R/getSubstrate.R
MD5
DESCRIPTION
man
man/getEntry.Rd
man/getPathway.Rd
man/getUGraph.Rd
man/all_genes.Rd
man/getUnknowReaction.Rd
man/NodeGeneData.Rd
man/ViewLatestTime.Rd
man/getSubtype.Rd
man/simplifyGraph.Rd
man/getProduct.Rd
man/AUCSC.Rd
man/getUnknowSubstrate.Rd
man/getSubstrate.Rd
man/getOrgAndIdType.Rd
man/node_gene.Rd
man/gene2ec.Rd
man/num_node_gene_score.Rd
man/getUnknowSubtype.Rd
man/getUnknowRelation.Rd
man/getUnknowProduct.Rd
man/UPDATE.Rd
man/TPEA.Rd
man/DownloadKGML.Rd
man/getNonMetabolicGraph.Rd
man/getRelation.Rd
man/TPEA-package.Rd
man/gene2ko.Rd
man/pathway_names.Rd
man/viewpathway.Rd
man/filterNode.Rd
man/keggGene2gene.Rd
man/getReaction.Rd
man/getKGeneFromKO.Rd
man/getSimpleGraph.Rd
man/mapNode.Rd
man/getGeneFromKGene.Rd
man/getKGeneFromEnzyme.Rd
man/NodeGene.Rd
man/getGraphics.Rd
man/getGeneFromEnzyme.Rd
man/importLatesData.Rd
man/PathNetwork.Rd
man/getGeneFromKO.Rd
INDEX
TPEA documentation built on May 19, 2017, 6:57 a.m.

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