\HeaderA{ROCDATA}{Transformation and other factors of the pairwise peak-lists
Comparsion Process}{ROCDATA}
\aliasA{msms.binary}{ROCDATA}{msms.binary}
\aliasA{msms.intensity}{ROCDATA}{msms.intensity}
\aliasA{pmf.binary}{ROCDATA}{pmf.binary}
\aliasA{pmf.intensity}{ROCDATA}{pmf.intensity}
\keyword{datasets}{ROCDATA}
\begin{Description}\relax
Scores of the binary and intensity based measures for PMF and MS/MS
datasets. The file contains the sensitivity and specificity PAUC obtained
for each set of factors. In addition it contains the
AUC and max(sum(specificity+sensitivity)). For an analysis of variance,
to determine the best performing measures see the Sweave file varan.Rnw
in the doc directory of the package.
\end{Description}
\begin{Usage}
\begin{verbatim}data(pmf.binary); data(pmf.intensity);data(msms.binary);data(msms.intensity)\end{verbatim}
\end{Usage}
\begin{Format}\relax
A dataframe with 10 columns and 96 (Binary) or rows.
\end{Format}
\begin{Details}\relax
Column names and they content.
\Itemize{
\item  ABBREV -- abreviation of CP
\item Measure -- Measure (dissimilarity measure)
\Itemize{
\item Binary -- measures.
\Itemize{
\item fm -- Fowlkes Mallows
\item hg -- Huberts Gamma
\item rmi -- relative mutual information
\item gower -- gower coefficient
}
\item Intensity --  based measures.
\Itemize{
\item cov -- Covariance
\item soai -- sum of agreeing intensities
\item euclidean -- euclidean distance
\item manhattan -- Manhattan distance
\item canberra -- Canberra distance
\item simindex -- similarity index
\item dotprod -- dot product measure
}
}
\item Trans (intensity transformation)
\Itemize{
\item N -- raw data
\item S -- square root transformation
\item L -- log transformation
\item R -- ranks of intensities
}
\item Scale -- scaling of peak intensities
\Itemize{
\item T -- total ion count scaling
\item N -- vector length
\item S -- root mean square
\item Z -- z-score        
}
\item theta -- weigth of non-matching peaks
\Itemize{
\item 0.5                         
\item 1                           
\item 2   
}
\item Weight -- weighting of measurement accuracy
\Itemize{
\item M -- without non-crossing matching                  
\item W -- with non-crossing matching     
}
\item Noncross (non-crossing matching)
\Itemize{
\item A -- the non-crossing matching was determined
\item O -- the non-crossing matching was not determined
}
\item Length -- length of aligned PLs
\Itemize{
\item N=0
\item N=250 (PMF) ; N=800 (MSMS)
}
\item AUC -- Area under the reveiver operator characteristic curve.
\item MaxSSp -- Maxiumum of sensitivity + specificity on the ROC
curve.
\item FPPAUC -- specificity PAUC.
\item TPPAUC -- sensitivity PAUC
}
\end{Details}
\begin{Source}\relax
\end{Source}
\begin{References}\relax
Wolski et al. "Transformation and other factors of the
peptide MS peak-list comparsion process"(2005) See doc directory of
this package
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(pmf.binary)
data(pmf.intensity)
data(msms.binary)
data(msms.intensity)
\end{ExampleCode}
\end{Examples}

