\HeaderA{SMAP-internal}{SMAP-internal}{SMAP.Rdash.internal}
\aliasA{A,eta-method}{SMAP-internal}{A,eta.Rdash.method}
\aliasA{A,grad-method}{SMAP-internal}{A,grad.Rdash.method}
\aliasA{A,SMAPHMM-method}{SMAP-internal}{A,SMAPHMM.Rdash.method}
\aliasA{chromosome,SMAPObservations-method}{SMAP-internal}{chromosome,SMAPObservations.Rdash.method}
\aliasA{endPosition,SMAPObservations-method}{SMAP-internal}{endPosition,SMAPObservations.Rdash.method}
\aliasA{HMM,SMAPProfile-method}{SMAP-internal}{HMM,SMAPProfile.Rdash.method}
\aliasA{initialize,eta-method}{SMAP-internal}{initialize,eta.Rdash.method}
\aliasA{initialize,gaussparam-method}{SMAP-internal}{initialize,gaussparam.Rdash.method}
\aliasA{initialize,grad-method}{SMAP-internal}{initialize,grad.Rdash.method}
\aliasA{initialize,SMAPHMM-method}{SMAP-internal}{initialize,SMAPHMM.Rdash.method}
\aliasA{initialize,SMAPObservations-method}{SMAP-internal}{initialize,SMAPObservations.Rdash.method}
\aliasA{initialize,SMAPProfile-method}{SMAP-internal}{initialize,SMAPProfile.Rdash.method}
\aliasA{name,SMAPObservations-method}{SMAP-internal}{name,SMAPObservations.Rdash.method}
\aliasA{name,SMAPProfile-method}{SMAP-internal}{name,SMAPProfile.Rdash.method}
\aliasA{name,SMAPProfiles-method}{SMAP-internal}{name,SMAPProfiles.Rdash.method}
\aliasA{noObservations,SMAPObservations-method}{SMAP-internal}{noObservations,SMAPObservations.Rdash.method}
\aliasA{noStates,SMAPHMM-method}{SMAP-internal}{noStates,SMAPHMM.Rdash.method}
\aliasA{observations,SMAPProfile-method}{SMAP-internal}{observations,SMAPProfile.Rdash.method}
\aliasA{observations,SMAPProfiles-method}{SMAP-internal}{observations,SMAPProfiles.Rdash.method}
\aliasA{P,SMAPProfile-method}{SMAP-internal}{P,SMAPProfile.Rdash.method}
\aliasA{Phi,eta-method}{SMAP-internal}{Phi,eta.Rdash.method}
\aliasA{Phi,grad-method}{SMAP-internal}{Phi,grad.Rdash.method}
\aliasA{Phi,SMAPHMM-method}{SMAP-internal}{Phi,SMAPHMM.Rdash.method}
\aliasA{Pi,eta-method}{SMAP-internal}{Pi,eta.Rdash.method}
\aliasA{Pi,grad-method}{SMAP-internal}{Pi,grad.Rdash.method}
\aliasA{Pi,SMAPHMM-method}{SMAP-internal}{Pi,SMAPHMM.Rdash.method}
\aliasA{plot,SMAPProfile,missing-method}{SMAP-internal}{plot,SMAPProfile,missing.Rdash.method}
\aliasA{plot,SMAPProfiles,missing-method}{SMAP-internal}{plot,SMAPProfiles,missing.Rdash.method}
\aliasA{Q,SMAPProfile-method}{SMAP-internal}{Q,SMAPProfile.Rdash.method}
\aliasA{Q,SMAPProfiles-method}{SMAP-internal}{Q,SMAPProfiles.Rdash.method}
\aliasA{reporterId,SMAPObservations-method}{SMAP-internal}{reporterId,SMAPObservations.Rdash.method}
\aliasA{show,SMAPHMM-method}{SMAP-internal}{show,SMAPHMM.Rdash.method}
\aliasA{show,SMAPObservations-method}{SMAP-internal}{show,SMAPObservations.Rdash.method}
\aliasA{show,SMAPProfile-method}{SMAP-internal}{show,SMAPProfile.Rdash.method}
\aliasA{show,SMAPProfiles-method}{SMAP-internal}{show,SMAPProfiles.Rdash.method}
\aliasA{smap,SMAPHMM,SMAPObservations-method}{SMAP-internal}{smap,SMAPHMM,SMAPObservations.Rdash.method}
\aliasA{startPosition,SMAPObservations-method}{SMAP-internal}{startPosition,SMAPObservations.Rdash.method}
\aliasA{value,eta-method}{SMAP-internal}{value,eta.Rdash.method}
\aliasA{value,SMAPObservations-method}{SMAP-internal}{value,SMAPObservations.Rdash.method}
\aliasA{[,SMAPObservations-method}{SMAP-internal}{[,SMAPObservations.Rdash.method}
\aliasA{[,SMAPProfile-method}{SMAP-internal}{[,SMAPProfile.Rdash.method}
\aliasA{[[<-,SMAPProfiles-method}{SMAP-internal}{[[<.Rdash.,SMAPProfiles.Rdash.method}
\keyword{methods}{SMAP-internal}
\keyword{internal}{SMAP-internal}
\begin{Description}\relax
Internal methods for the \pkg{SMAP} package.
\end{Description}
\begin{Author}\relax
Robin Andersson, \email{robin.andersson@lcb.uu.se}
\end{Author}
\begin{References}\relax
Andersson, R., Bruder, C. E. G., Piotrowski, A., Menzel, U., Nord, H.,
Sandgren, J., Hvidsten, T. R., Diaz de Stahl, T., Dumanski, J. P.,
Komorowski, J., A Segmental Maximum A Posteriori Approach to Array-CGH
Copy Number Profiling, submitted
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{smap}{smap}}
\end{SeeAlso}

