A Novel Topology-Based Pathway Enrichment Analysis Approach
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘TPEA’ version 3.1.0
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. |