miR2Pathway is a PageRank-based method that can be used to rank disease risk of miRNA-mediated biological pathways. miR2Pathway can help explore how much miRNAs differentially influence the activity of biological pathways between two classes of phenotypes
For information about the method, please read:
Chaoxing Li and Valentin Dinu. “miR2Pathway: A Novel Analytical Method to Discover MicroRNA-mediateding Dysregulated Pathways Involved in Disease”, 2017.
R code, sample data and sample scripts
The R script to carry out miR2Pathway is available here:
The R script to perform miR2Pathway
Example usage of miR2Pathway.R
Data used in miR2Pathway-example.R
miR2Pathway <- function(mydata.gene,mydata.miR,genelist,name.genelist,miRlist,miRlist.full,N.miR,N.gene,N.path,Num.sample.normal,Num.sample.case,Pathway.database,cor.cutoff,N.parallel)
|mydata.gene:||a gene expression dataset (matrix). Rows represent genes, and columns represent samples (from control to case).|
|mydata.miR:||a miRNA expression dataset (matrix). Rows represent miRNAs, and columns represent samples (from control to case)|
|genelist:||a list of gene names (e.g., gene symobol).|
|name.genelist:||a matrix of gene expression dataset (The order of gene names must be consistent with genelist). This matrix is 1*N, where N is the number of genes. The value of each element could be a ramdom value. See an example in Examples Section.|
|miRlist:||miRNA in a standard format|
|miRlist.full:||the full name of all miRNAs.|
T.score: the total differential influence of all the miRNAs on the activity of a single pathway between control and case.
LengthOfPathway: gene counts of pathways.
# An example for the matrix of name.genelist:
# 100130426 100133144 100134869 10357 10431 136542
# Sample1 0 0 0 0 0 0
Authors: Chaoxing Li and Valentin Dinu
If you use or modify the code, please cite:
“miR2Pathway: A Novel Analytical Method to Discover MicroRNA-mediateding Dysregulated Pathways Involved in Disease”, 2017.
Please email Chaoxing Li <firstname.lastname@example.org> or Valentin Dinu <Valentin.Dinu@asu.edu> if you have any questions, concerns or feedback.
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