\section{Data access}\label{dataAccess}

The interaction matrix can be loaded by 
<<dataAcceess1,results=hide>>=
library("HD2013SGI")
data("Interactions", package="HD2013SGI")
@ 

The element \Robject{Interactions\$piscore} of this data object is a 6-dimensional array of
$\pi$-scores, \Robject{Interactions\$padj} is a 5-dimensional
array of BH-adjusted p-values, and \Robject{Interactions\$Anno}
contains annotation for target genes, query genes, and phenotypes.
You can type
<<dataAccess2,eval=FALSE>>=
? Interactions
@
to see the documentation of this data object. Similarly, you can use
the \Robject{?} operator to obtain help on any of the below data objects; 
The following datasets are available:
\begin{itemize}
  \item {\bf Interactions} The genetic interaction data ($\pi$-scores,
    p-values, and annotation). {\bf This is the main data source of this package.}
  \item {\bf featuresPerWell} The screen data in screen order.
  \item {\bf datamatrixfull} The phenotype data of all pairwise genetic
    perturbation experiments before quality control and feature selection.
  \item {\bf QueryAnnotation} Annotation of all the query genes in the screen.
  \item {\bf TargetAnnotation} Annotation of all target genes in the screen.
  \item {\bf stabilitySelection} Results from the feature selection step.
  \item {\bf datamatrix} The phenotype data of all pairwise genetic perturbation
    experiments after quality control and feature selection.
  \item {\bf mainEffects} Estimated main effects (single knock down effect).
  \item {\bf nrOfInteractionsPerTarget} Number of interactions per target gene.
\end{itemize}
They are intermediate results of the analysis steps described in the
following, precomputed and loadable for convenience.