Description
`FindSubPath` uses a greedy search algorithm to search for key subpathways in each entire pathway.
Usage
FindSubPath(
zz,
Pathway = "kegg",
delta = 0.05,
seed_p = 0.05,
min.size = 5,
out.F = FALSE,
out.file = "Subpath.txt"
)
Value
Key dysfunctional subpathways in each pathway, in which the risk score of the genes were significantly higher.
Arguments
- zz
A numeric vector of z_scores.
- Pathway
The name of the pathway database.
- delta
Diffusion coefficient in each step of searching subpath.
- seed_p
Define gene whose p-value smaller than seed_p as seed gene.
- min.size
The smallest size of subpathways.
- out.F
Logical,tell if output subpathways.
- out.file
file name of subpathways.
Examples
Run this coderequire(graphite)
zz<-GetExampleData("zzz")
k<-FindSubPath(zz)
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