Adjacency {dhga}

Construction of Gene Co-expression Network

Description

The function computes the adjacency matrix using the soft threshold parameter to construct a Gene Co-expression Network

Usage

Adjacency(x, beta, threshold)

Arguments

x

x is a data frame of gene expression values where rows represent genes and columns represent samples/time points under a particular condition/stress/trait.

beta

beta is a soft threshold parameter determined from the scale free property of biological networks (Gene Co-expression Network).

threshold

threshold is a scalar representing the threshold value for the adjacency matrix to construct the Gene Co-expression Network.

Value

The function returns a list of outputs like adjacency matrix, Node-list and Edge-list for constructing a Gene Co-expression Network at certain threshold level

Author(s)

Samarendra Das and Baidya Nath Mandal

Examples

data(rice_normal)
beta=6
threshold=0.4
Adjacency(rice_normal,6,0.4)