Permutation: Permutation

In ICDS: Identification of Cancer Dysfunctional Subpathway with Omics Data

Description

the permutation test method 1 and method 2 were used to calculate the statistical significance level for these optimal subpathways.

Usage

Permutation(
  subpathwayz,
  zz,
  nperm1 = 1000,
  method1 = TRUE,
  nperm2 = 1000,
  method2 = FALSE
)

Arguments

subpathwayz	Optimize intersted subpathways
zz	a vector of z-scores
nperm1	times of permutation to perform use method1
method1	permutation analysis method1
nperm2	times of permutation to perform use method2
method2	permutation analysis method2

Value

the statistical significance p value and FDR for these optimal subpathways

Examples

require(graphite)
keysubpathways<-GetExampleData("keysubpathways")
zzz<-GetExampleData("zzz")
Permutation(keysubpathways,zzz,nperm1=10,method1=TRUE,nperm2=10,method2=FALSE)

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