--- a
+++ b/man/permutation_pc.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helper_function.R
+\name{permutation_pc}
+\alias{permutation_pc}
+\title{Permutations to build differential network based on partial correlation analysis}
+\usage{
+permutation_pc(
+  m,
+  p,
+  n_group_1,
+  n_group_2,
+  data_group_1,
+  data_group_2,
+  rho_group_1_opt,
+  rho_group_2_opt
+)
+}
+\arguments{
+\item{m}{This is the number of permutations.}
+
+\item{p}{This is the number of biomarker candidates.}
+
+\item{n_group_1}{This is the number of subjects in group 1.}
+
+\item{n_group_2}{This is the number of subjects in group 2.}
+
+\item{data_group_1}{This is a \eqn{n*p} matrix containing group 1 data.}
+
+\item{data_group_2}{This is a \eqn{n*p} matrix containing group 2 data.}
+
+\item{rho_group_1_opt}{This is an optimal tuning parameter to obtain a sparse differential 
+network for group 1.}
+
+\item{rho_group_2_opt}{This is an optimal tuning parameter to obtain a sparse differential
+network for group 2.}
+}
+\value{
+A multi-dimensional matrix that contains the permutation result.
+}
+\description{
+A permutation test that randomly permutes the sample labels in distinct
+    biological groups for each biomolecule. The difference in paired partial correlation
+    is considered statistically significant if it falls into the 2.5% tails on either end of the 
+    empirical distribution curve.
+}