FindSubPath: FindSubPath

In ICDS: Identification of Cancer Dysfunctional Subpathway with Omics Data

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)

ICDS documentation built on July 15, 2021, 5:06 p.m.