ICDS (version 0.1.3)

Permutation: Permutation

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
)

Value

the statistical significance p value and FDR for these optimal subpathways

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

Examples

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