AnnotateExtra	AnnotateExtra-ExomeDepth-method
AnnotateExtra,ExomeDepth-method	AnnotateExtra-ExomeDepth-method
CallCNVs	CallCNVs-ExomeDepth-method
CallCNVs,ExomeDepth-method	CallCNVs-ExomeDepth-method
Conrad.hg19.common.CNVs	Conrad.hg19.common.CNVs
count.everted.reads	count.everted.reads
countBam.everted	countBam.everted
countBamInGRanges.exomeDepth	countBamInGRanges.exomeDepth
C_hmm	C_hmm
ExomeCount	ExomeCount
ExomeDepth-class	ExomeDepth-class
exons.hg19	exons.hg19
exons.hg19.X	exons.hg19.X
genes.hg19	genes.hg19
get.power.betabinom	get.power.betabinom
getBamCounts	getBamCounts
get_loglike_matrix	get_loglike_matrix
initialize,ExomeDepth-method	initialize-ExomeDepth-method
plot,ANY-method	plot-methods
plot,ExomeDepth,ANY-method	plot-methods
plot,ExomeDepth-method	plot-methods
plot-methods	plot-methods
plot.ExomeDepth	plot-methods
qbetabinom	qbetabinom
qbetabinom.ab	qbetabinom.ab
select.reference.set	select.reference.set
somatic.CNV.call	somatic.CNV.call
TestCNV	TestCNV-ExomeDepth-method
TestCNV,ExomeDepth-method	TestCNV-ExomeDepth-method
viterbi.hmm	viterbi.hmm
