A	SMAPHMM-class
A,eta-method	SMAP-internal
A,grad-method	SMAP-internal
A,SMAPHMM-method	SMAP-internal
chromosome	SMAPObservations-class
chromosome,SMAPObservations-method	SMAP-internal
endPosition	SMAPObservations-class
endPosition,SMAPObservations-method	SMAP-internal
GBM	GBM
HMM	SMAPProfile-class
HMM,SMAPProfile-method	SMAP-internal
initialize,eta-method	SMAP-internal
initialize,gaussparam-method	SMAP-internal
initialize,grad-method	SMAP-internal
initialize,SMAPHMM-method	SMAP-internal
initialize,SMAPObservations-method	SMAP-internal
initialize,SMAPProfile-method	SMAP-internal
name	SMAPObservations-class
name,SMAPObservations-method	SMAP-internal
name,SMAPProfile-method	SMAP-internal
name,SMAPProfiles-method	SMAP-internal
noObservations	SMAPObservations-class
noObservations,SMAPObservations-method	SMAP-internal
noStates	SMAPHMM-class
noStates,SMAPHMM-method	SMAP-internal
observations	SMAPProfile-class
observations,SMAPProfile-method	SMAP-internal
observations,SMAPProfiles-method	SMAP-internal
P	SMAPProfile-class
P,SMAPProfile-method	SMAP-internal
Phi	SMAPHMM-class
Phi,eta-method	SMAP-internal
Phi,grad-method	SMAP-internal
Phi,SMAPHMM-method	SMAP-internal
Pi	SMAPHMM-class
Pi,eta-method	SMAP-internal
Pi,grad-method	SMAP-internal
Pi,SMAPHMM-method	SMAP-internal
plot,SMAPObservations,missing-method	SMAPObservations-class
plot,SMAPProfile,missing-method	SMAP-internal
plot,SMAPProfiles,missing-method	SMAP-internal
Q	SMAPProfile-class
Q,SMAPProfile-method	SMAP-internal
Q,SMAPProfiles-method	SMAP-internal
reporterId	SMAPObservations-class
reporterId,SMAPObservations-method	SMAP-internal
show,SMAPHMM-method	SMAP-internal
show,SMAPObservations-method	SMAP-internal
show,SMAPProfile-method	SMAP-internal
show,SMAPProfiles-method	SMAP-internal
smap	smap
smap,SMAPHMM,SMAPObservations-method	SMAP-internal
SMAPHMM	SMAPHMM
SMAPHMM-class	SMAPHMM-class
SMAPObservations	SMAPObservations
SMAPObservations-class	SMAPObservations-class
SMAPProfile-class	SMAPProfile-class
SMAPProfiles-class	SMAPProfiles-class
startPosition	SMAPObservations-class
startPosition,SMAPObservations-method	SMAP-internal
value	SMAPObservations-class
value,eta-method	SMAP-internal
value,SMAPObservations-method	SMAP-internal
[,SMAPObservations-method	SMAP-internal
[,SMAPProfile-method	SMAP-internal
[[<-,SMAPProfiles-method	SMAP-internal
