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TPEA (version 3.1.0)

A Novel Topology-Based Pathway Enrichment Analysis Approach

Description

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.

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Version

Install

install.packages('TPEA')

Monthly Downloads

190

Version

3.1.0

License

GPL-2

Maintainer

Wei Jiang

Last Published

June 25th, 2017

Functions in TPEA (3.1.0)

ViewLatestTime

Check up the latest date of KGML files
all_genes

All human protein coding genes
gene2ko

The relationship of genes and KO
getEntry

Obtain the nodes
getSubtype

Get the type of nodes
getUGraph

Obtain the graph of pathways
node_gene

The relationship between nodes and genes
num_node_gene_score

The score of each node in a certain pathway
NodeGene

Restract the relationship between nodes and genes.
NodeGeneData

Intergate list of node,gene and the score of node.
getGeneFromKO

Obtain the genes from KO
getGraphics

Recontructe the network based on pathways
getSimpleGraph

Obtain the graph of pathways
PathNetwork

Reconstruct pathways to networks
TPEA-package

TPEA: A Novel Pathway enrichment analysis approach based on topological structure and updated annotation of pathway
getGeneFromEnzyme

Obtain the genes from enzymes
getGeneFromKGene

Obtain the genes from KGenes
getReaction

Get the reaction of nodes in pathways
getRelation

Get the relation of nodes in pathways
getUnknowRelation

Get the relation of nodes in pathways
TPEA

Statistical test and calculate the significance
UPDATE

Update the latest data from KEGG database
filterNode

Filter the nodes in pathways
gene2ec

The relationship of genes and EC
getNonMetabolicGraph

Convert the non-metaboloc pathway to network
getUnknowSubstrate

Obtain the information about nodes in KEGG database
getOrgAndIdType

Get the type names of nodes
keggGene2gene

KeggGene to genes
mapNode

Obtain the relationship of nodes and genes
AUEC

Calculate the area under the cumulative enrichment curve (AUEC) based on the interested gene set.
DownloadKGML

Download the latest KGML files
getKGeneFromEnzyme

Obtain genes from KGnenes
getKGeneFromKO

Obtain the genes from KO
getPathway

Get the pathway from KEGG database.
getSubstrate

Obtain the information about nodes in KEGG database
getUnknowProduct

Get the products
getUnknowReaction

Get the reaction of nodes in pathways
pathway_names

Pathway names in KEGG Database
simplifyGraph

Recontructe the network based on pathways
getProduct

Get the products
getUnknowSubtype

Obtain the types of genes in pathways
importLatesData

Import the latest relationship information.
viewpathway

The visualization of interested pathway based on the genes you input, such as differentially expressed genes.