\name{SMAP-internal} \docType{methods} \alias{A,grad-method} \alias{A,eta-method} \alias{Phi,grad-method} \alias{Phi,eta-method} \alias{Pi,grad-method} \alias{Pi,eta-method} \alias{initialize,grad-method} \alias{initialize,eta-method} \alias{initialize,gaussparam-method} \alias{value,eta-method} \alias{P,SMAPProfile-method} \alias{Q,SMAPProfile-method} \alias{Q,SMAPProfiles-method} \alias{HMM,SMAPProfile-method} \alias{initialize,SMAPProfile-method} \alias{observations,SMAPProfile-method} \alias{observations,SMAPProfiles-method} \alias{show,SMAPProfile-method} \alias{show,SMAPProfiles-method} \alias{name,SMAPProfile-method} \alias{name,SMAPProfiles-method} \alias{[,SMAPProfile-method} \alias{[,SMAPObservations-method} \alias{[[<-,SMAPProfiles-method} \alias{chromosome,SMAPObservations-method} \alias{endPosition,SMAPObservations-method} \alias{initialize,SMAPObservations-method} \alias{name,SMAPObservations-method} \alias{noObservations,SMAPObservations-method} \alias{reporterId,SMAPObservations-method} \alias{show,SMAPObservations-method} \alias{startPosition,SMAPObservations-method} \alias{value,SMAPObservations-method} \alias{A,SMAPHMM-method} \alias{Phi,SMAPHMM-method} \alias{Pi,SMAPHMM-method} \alias{initialize,SMAPHMM-method} \alias{noStates,SMAPHMM-method} \alias{show,SMAPHMM-method} \alias{smap,SMAPHMM,SMAPObservations-method} \alias{plot,SMAPProfile,missing-method} \alias{plot,SMAPProfiles,missing-method} \title{SMAP-internal} \description{Internal methods for the \pkg{SMAP} package.} \seealso{ \code{\link[SMAP:smap]{smap}} } \author{Robin Andersson, \email{robin.andersson@lcb.uu.se}} \references{ 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 } \keyword{methods} \keyword{internal}