FindSubPath {ICDS}

FindSubPath

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"
)

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.

Value

Key dysfunctional subpathways in each pathway, in which the risk score of the genes were significantly higher.

Examples

require(graphite)
zz<-GetExampleData("zzz")
k<-FindSubPath(zz)