R: A Novel Topology-Based Pathway Enrichment Analysis Approach

# A Novel Topology-Based Pathway Enrichment Analysis Approach

## Documentation for package ‘TPEA’ version 3.1.0

- DESCRIPTION file

## Help Pages

TPEA-package | TPEA: A Novel Pathway enrichment analysis approach based on topological structure and updated annotation of pathway
all_genes | All human protein coding genes
AUEC | Calculate the area under the cumulative enrichment curve (AUEC) based on the interested gene set.
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
NodeGene | Restract the relationship between nodes and genes.
NodeGeneData | Intergate list of node,gene and the score of node.
node_gene | The relationship between nodes and genes
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
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 you input, such as differentially expressed genes.