fisher_test.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/fisher_test.R
\name{fisher_test}
\alias{fisher_test}
\title{Function to compute fisher z-transformation pvalues for the links}
\usage{
fisher_test(score_matrix, alpha, nsamp, nvar)
}
\arguments{
\item{score_matrix}{score matrix obtained from DPM or reg.DPM.}

\item{alpha}{a significance level}

\item{nsamp}{is the number of samples (number of rows of input matrix for (reg-)DPM ). Note that we need nsamp such that: nsamp*(nsamp+1)> 2*(nvar-5)}

\item{nvar}{is the number of variables (number of columns of input matrix for (reg-)DPM )}
}
\value{
a list containing
- the list of significant links as a data frame. Each line of the data frame corresponds to a link.
The first and second columns are the corresponding nodes of the link, the third column is the score of the link and the forth column is the corresponding pvalue.
- the threshold that all the links with scores more than it are significant at defined significance level.
}
\description{
Function to compute fisher z-transformation pvalues for the links
}
\examples{
## Load DREAM4 data (insilico_size10_1_knockouts)
data(dream4)

## Run regularized DPM
res <- reg.dpm(data)

## Get the list of significant links at significance level alpha=0.05
fisher_test(res,alpha=0.05,10,10)$LinkList

##Get the threshold at significance level alpha=0.05
fisher_test(score_matrix=res,alpha=0.05,nsamp=10,nvar=10)$threshold


}