pvalue.hub {dhga}

Compuation of gene connection sigificance values in a Gene Co-expression network

Description

The function computes ths statisical significance values of gene connections in a GCN for a particular condition/trait/stress

Usage

pvalue.hub(x, beta, m, s, plot=TRUE)

Arguments

x

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

beta

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

m

m is a scalar representing sample size and is less than or equal to number of columns in x.

s

s is a scalar representing number of times each of the m samples will be resampled.

plot

plot is a character must either take logical value TRUE/FALSE representing whether the plot of the pvalues of gene connections of all genes in Gene Co-expression Network needs to be constructed or not.

Value

The function returns a vector of p-values for all the genes in the GCN

Author(s)

Samarendra Das and Baidya Nath Mandal

Examples

data(rice_salt)
x=as.data.frame(rice_salt)
beta=6
m=18
s=80
pvalue.hub(x, beta, m, s, plot=TRUE)