tileHMM-package	tileHMM-package
as.data.frame.discDist	dist-access
as.matrix.discDist	dist-access
as.vector.discDist	dist-access
backward	forward
backward,hmm-method	forward
baumWelch	baumWelch
baumWelch,hmm,list-method	baumWelch
contDist-class	contDist-class
contHMM-access	contHMM-access
contHMM-class	contHMM-class
discDist-class	discDist-class
dist-class	dist-class
forward	forward
forward,hmm-method	forward
generate.data	generate.data
getHMM	getHMM
gff2index	gff2index
hmm-class	hmm-class
hmm.setup	hmm.setup
initialize,contDist-method	initializeDist-methods
initialize,contHMM	contHMM-class
initialize,contHMM-method	initializeHMM-methods
initialize,discDist-method	initializeDist-methods
initialize,tDist-method	initializeDist-methods
internals	internals
length,discDist-method	dist-access
length,hmm-method	contHMM-access
logSum	logSum
new,contDist-method	initializeDist-methods
new,contHMM-method	initializeHMM-methods
new,discDist-method	initializeDist-methods
new,tDist-method	initializeDist-methods
plot	plot
plot.contDist	plot
plot.contHMM	plot
plot.tDist	plot
posterior	posterior
reg2gff	reg2gff
region.length	region.length
region.position	region.position
remove.short	remove.short
sampleObs	sampleObs
sampleObs,discDist,numeric-method	sampleObs
sampleObs,tDist,numeric-method	sampleObs
sampleSeq	sampleSeq
sampleSeq,contHMM,numeric-method	sampleSeq
show,contDist-method	contDist-class
show,hmm-method	hmm-class
shrinkt.st	shrinkt.st
simChIP	simChIP
states	states
states,hmm-method	states
tDist-class	tDist-class
tileHMM	tileHMM-package
viterbi	viterbi
viterbi,hmm-method	viterbi
viterbiEM	viterbiEM
viterbiTraining	viterbiTraining
viterbiTraining,hmm,list-method	viterbiTraining
[.contDist	dist-access
[.contHMM	contHMM-access
[.discDist	dist-access
[.tDist	dist-access
[<-.contDist	dist-access
[<-.tDist	dist-access
[[.discDist	dist-access
_backward	internals
_baumWelch_trans	internals
_forward	internals
_get_obs_prob	internals
_log_sum	internals
_viterbi	internals
