\section{Distribution of positive and negative interactions}\label{distributionOfInteractions}
\subsection{Preliminaries}

<<distributionOfInteractions1>>=
library("HD2013SGI")

data("Interactions",package="HD2013SGI")
data("mainEffects",package="HD2013SGI")
data("nrOfInteractionsPerTarget",package="HD2013SGI")

dir.create(file.path("result","Figures"),showWarnings=FALSE,recursive=TRUE)
@

\subsection{Distribution of interactions}
The mean of the interaction scores was taken over the two replicates.
<<distributionOfInteractions2,results=hide>>=
PI = Interactions$piscore
PI = (PI[,,,,,1]+PI[,,,,,2]) / 2
@
%
The number of positive and negative interactions for each
phenotypic feature was counted. Only significant interactions (FDR <=
0.01) were considered.
%
<<distributionOfInteractions3,results=hide>>=
npos = rep(NA_integer_, dim(PI)[5])
nneg = rep(NA_integer_, dim(PI)[5])
for (i in seq_len(dim(PI)[5])) {
  I = which(Interactions$padj[,,,,i] <= 0.01)
  pi = (PI[,,,,i])[I]
  npos[i] = sum(pi >= 0)
  nneg[i] = sum(pi < 0)
}
@
%
\Robject{npos} (\Robject{nneg}) contains the number of positive
(negative) genetic interactions per phenotypic feature. The features
were sorted by the total number (positive and negative) interactions starting
with the largest number.
%
<<distributionOfInteractions4,results=hide>>=
I = order(-(npos+nneg))
npos = npos[I]
nneg = nneg[I]
@
A barchart was plotted showing the number of positive and negative interactions.
<<distributionOfInteractions5,echo=FALSE,results=hide>>=
pdf(file.path("result","Figures","distributionOfInteractions.pdf"),
    width=5,height=5)
<<distributionOfInteractions6,results=hide>>=
barplot(rbind(npos,nneg),beside=TRUE,
        col=HD2013SGI:::Colors[c(3,1)],
        xlab="phenotypic features",ylab="number of interactions")
legend("topright",legend=c("pos. interactions", "neg. interactions"),
       fill=HD2013SGI:::Colors[c(3,1)])
<<distributionOfInteractions7,echo=FALSE,results=hide>>=
dev.off()
@

\begin{center}
  \includegraphics[width=0.7\textwidth]{result/Figures/distributionOfInteractions.pdf}
\end{center}