| Type: | Package |
| Title: | A Novel Topology-Based Pathway Enrichment Analysis Approach |
| Version: | 3.1.0 |
| Date: | 2017-6-25 |
| Author: | Wei Jiang |
| Maintainer: | Wei Jiang <jiangwei@hrbmu.edu.cn> |
| 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. |
| License: | GPL-2 |
| Depends: | R (≥ 2.10), MESS, Matrix, foreach |
| Imports: | XML, RCurl, utils, igraph |
| Suggests: | geeM, geepack |
| LazyData: | true |
| LazyLoad: | yes |
| NeedsCompilation: | no |
| Packaged: | 2017-06-25 01:36:20 UTC; Administrator |
| Repository: | CRAN |
| Date/Publication: | 2017-06-25 15:42:32 UTC |
TPEA: A Novel Pathway enrichment analysis approach based on topological structure and updated annotation of pathway
Description
This package descirbed A Novel Pathway enrichment analysis approach based on topological structure and updated annotation of pathway which integrated the topological property of the pathway and the global position of nodes in pathways.Additionally,it also provided the update functions which could obtain the latest pathway information from KEGG database and users can use the latest information to do the pathway enrichment analysis.
Details
The function AUEC is to calculate the area under the cumulative enrichment curve. The function TPEA is to measure the significance of pathways. The function UPDATE is to online download the latest KEGG pathway information. The viewpathway function is to visualize the pathway in the result based on the genes you input, such as differentially expressed genes. Several other functions are the update related functions, including ViewUpdateTime,UpdateKGML,PathNetwork,NodeGeneData,NodeGene,importUpdateData. The functions involved in relationship between nodes and genes were provided by Chunquan Li. If you want to use the latest information of KEGG database,please run "UPDATE()" functions first, and then run the pathway enrichment analysis functions AUEC and TPEA.
Author(s)
Wei Jiang
Calculate the area under the cumulative enrichment curve (AUEC) based on the interested gene set.
Description
The interested gene set may be the differentially expressed genes or any other gene set. The function calculate the AUEC based on the interested genes. AUEC is the area under the cumulative enrichment curve in a coordinate system. X-axis displays the nodes by the scores from maximum to minimum. Y-axis displays the cumulative enrichment curve.
Usage
AUEC(DEGs)
Arguments
DEGs |
The interested genes you input and the format must be "Entrez ID". If not,translate the interested genes into Entrez ID. |
Details
The function only identifies Entrez ID of genes. The nodes are sorted by their AUEC in the pathway. If genes locates on the upstream or the nodes with high degree in a certain pathway, the AUEC of this pathway is high.
Value
The AUEC of 109 pathways based on the interested gene set.
Author(s)
Wei Jiang
Examples
##Randomly generated interested genes
DEGs<-sample(100:100000,15)
DEG<-as.matrix(DEGs);
## The function is used to calculate the observed statistic
area<-AUEC(DEG);
Download the latest KGML files
Description
Download the latest KGML files from KEGG database if you want the latest KGML files from KEGG database.
Details
Download the latest KGML files from KEGG database before pathway enrichment analysis.
Value
The latest KGML files from KEGG database.
Author(s)
Wei Jiang
Restract the relationship between nodes and genes.
Description
Restract the relationship between nodes and genes from KGML files.
Usage
NodeGene()
Details
This function must be used behind the function NodeGeneData.
Value
Restract the relationship between nodes and genes in each network based on the information of KGML files.
Author(s)
Wei Jiang
Intergate list of node,gene and the score of node.
Description
Intergate list of node,gene and the score of node based on latest KGML files from KEGG database.
Usage
NodeGeneData()
Details
Intergate list of node,gene and the score of node based on latest KGML files from KEGG database.
Value
List contains the relationship of node,gene and the score of node based on latest KGML files.
Author(s)
Wei Jiang
Reconstruct pathways to networks
Description
Reconstruct pathways to networks based on KGML files from KEGG database.
Usage
PathNetwork()
Details
Reconstruct pathways to networks based on KGML files from KEGG database.
Value
The relationship of edges in network.
Author(s)
Wei Jiang
Statistical test and calculate the significance
Description
Comparing with the AUEC_R which the interested gene set extract from the background gene set randomly and the corresponding AUEC based on interested gene set you input. The last step is to calculate the significance.
Usage
TPEA(DEGs, scores, n, FDR_method)
Arguments
DEGs |
Interested gene set such as differentailly expressed gene set. |
scores |
The "AUEC" based on the interested gene set of 109 pathways. |
n |
Randomly number,e.g. 1000, 5000. |
FDR_method |
The methods of calculating FDR value,e.g. "fdr","BH","BY" ,"bonferroni" and etc.. |
Details
To calculate the significance of the result, you can set "n" as "1000" or any other number you want.
Value
The ultimately result of this topology-based enrichment analysis method.
Author(s)
Wei Jiang
Examples
##Randomly generated interested gene set
ViewLatestTime()
##If you want to use the latest information,please run "UPDATE()".
DEGs<-sample(100:10000,10);
DEG<-as.matrix(DEGs);
##Set the times of perturbation
number<-50;
##Calculate the observed statistic
scores<-AUEC(DEG);
##Significant computational
FDR_method<-"fdr";
results<-TPEA(DEG,scores,number,FDR_method);
Update the latest data from KEGG database
Description
Updating the latest information of pathways in KEGG database and the time of this process is about 1-2 minutes.
Check up the latest date of KGML files
Description
Check up the latest date of KGML files from KEGG database.
Usage
ViewLatestTime()
Value
The latest date of KGML files from KEGG database.
Author(s)
Wei Jiang
All human protein coding genes
Description
Human protein coding genes from NCBI Database. We use this set as background gene set.
Filter the nodes in pathways
Description
Filter the nodes in pathways.
Author(s)
Wei Jiang
The relationship of genes and EC
Description
The relationship of genes and EC.
The relationship of genes and KO
Description
The relationship of genes and KO.
Obtain the nodes
Description
Processe the pathways
Obtain the genes from enzymes
Description
Processe the pathways
Obtain the genes from KGenes
Description
Processe the pathways
Obtain the genes from KO
Description
Processe the pathways
Recontructe the network based on pathways
Description
Processe the pathways
Obtain genes from KGnenes
Description
Processe the pathways
Obtain the genes from KO
Description
Processe the pathways
Convert the non-metaboloc pathway to network
Description
Processe the pathways
Get the type names of nodes
Description
Processe the pathways
Get the pathway from KEGG database.
Description
Processe the pathways
Get the products
Description
Processe the pathways
Get the reaction of nodes in pathways
Description
Processe the pathways
Get the relation of nodes in pathways
Description
Processe the pathways
Obtain the graph of pathways
Description
Processe the pathways
Obtain the information about nodes in KEGG database
Description
Processe the pathways
Get the type of nodes
Description
Processe the pathways
Obtain the graph of pathways
Description
Obtain the graph of pathways.
Usage
getUGraph(graphList, simpleGraph = TRUE)
Arguments
graphList |
Get the list. |
simpleGraph |
Convert the network. |
Value
The graphList relationship.
Author(s)
Wei Jiang
Get the products
Description
Processe the pathways
Get the reaction of nodes in pathways
Description
Processe the pathways
Get the relation of nodes in pathways
Description
Processe the pathways
Obtain the information about nodes in KEGG database
Description
Processe the pathways
Obtain the types of genes in pathways
Description
Processe the pathways
Author(s)
Wei Jiang
Import the latest relationship information.
Description
Import the latest relationship information about node,gene and score.
Usage
importLatesData()
Details
Import the latest relationship information about nodes,genes and their scores based on KGML files.
Value
Import the latest relationship information about node,gene and score.
Author(s)
Wei Jiang
KeggGene to genes
Description
Processe the pathways
Obtain the relationship of nodes and genes
Description
Processe the pathways
The relationship between nodes and genes
Description
The relationship between nodes and genes in each pathway in KEGG Database
The score of each node in a certain pathway
Description
The dataset includes 109 list and each list contains four columns (the order of node, node, gene and the score).
Pathway names in KEGG Database
Description
All pathway names we used in this method
Recontructe the network based on pathways
Description
Processe the pathways
The visualization of interested pathway based on the genes you input, such as differentially expressed genes.
Description
Input the number of the interested pathway in KEGG Database and genes you interested in, such as differentially expressed genes.
Usage
viewpathway(pathwayID, DEGs)
Arguments
pathwayID |
The number of interested pathway ID in KEGG Database, such as "hsa05210". |
DEGs |
The genes you interested in, such as differentially expressed genes. |
Details
The "DEGs" must be Entrez ID. If not, please translate them into Entrez ID.
Value
The interface link to KEGG Database to visualize the pathway you input.
Author(s)
Wei Jiang
Examples
DEGs<-c(836,842,5594,595);
DEG<-as.data.frame(DEGs);
pathwayID<-"hsa05210";
viewpathway(pathwayID,DEG);