PoTRA: Pathways of Topological Rank Analysis
Description
PoTRA is a PageRank-based method that can be used to detect pathways involved in disease.
For information about the method, please read:
Chaoxing Li, Li Liu and Valentin Dinu. “Pathways of Topological Rank Analysis (PoTRA): A Novel Method to Detect Pathways Involved in Cancer”, 2018.
R code, sample data and sample scripts
The R script to carry out PoTRA is available here:
The R script to perform the main part (Fisher’s exact test) of PoTRA, the alternative part (K.S. test) of PoTRA, and the overlay plot of kernel density for the PR scores.
Example usage of PoTRA.R
Data used in PoTRA-example.R
Usage
For PoTRA (Fisher’s exact test and K.S. test) based on correlation networks:
PoTRA.cor <- function(mydata,genelist,Num.sample.normal,Num.sample.case,Pathway.database, PR.quantile)
For PoTRA (Fisher’s exact test and K.S. test) based on combined networks:
PoTRA.comb <- function(mydata,genelist,Num.sample.normal,Num.sample.case,Pathway.database)
For the kernel density plot:
results.plot <- overlayplot(mydata,genelist,Num.sample.normal,Num.sample.case,Pathway.database)
Arguments
mydata: | a gene expression dataset (matrix). Rows represent genes, and columns represent samples (from control to case) |
genelist: | a list of gene names |
Num.sample.normal: | the number of normal samples |
Num.sample.case: | the number of cancer samples |
Pathway.database: | the pathway database used in the study, such as, KEGG, Biocarta and Reactome |
PR.quantile: | The percentile of PageRank scores as a cutoff for hub genes |
Value
Fishertest.p.value: the p-value of the Fisher’s exact test.
KStest.p.value: the p-value of the K.S. test.
LengthOfPathway: the length of pathways.
TheNumberOfHubGenes.normal: the number of hub genes for normal samples.
TheNumOfHubGene.case: the number of hub genes for cancer samples.
TheNumberOfEdges.normal: the number of edges in the network for normal samples.
TheNumberOfEdges.case: the number of edges in the network for cancer samples.
Examples
See PoTRA-example.R
Credits
Authors: Chaoxing Li, Li Liu and Valentin Dinu
If you use or modify the code, please cite:
“Pathways of Topological Rank Analysis (PoTRA): A Novel Method to Detect Pathways Involved in Cancer”, 2018.
Issues?
Please email Chaoxing Li <chaoxing@asu.edu> or Valentin Dinu <Valentin.Dinu@asu.edu> if you have any questions, concerns or feedback.
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