deepSNV-package	deepSNV-package
bam2R	bam2R
bbb	shearwater
betabinLRT	betabinLRT
bf2Vcf	bf2Vcf
consensusSequence	consensusSequence-methods
consensusSequence,deepSNV-method	consensusSequence-methods
consensusSequence,matrix-method	consensusSequence-methods
control	control-methods
control,deepSNV-method	control-methods
coordinates	coordinates-methods
coordinates,deepSNV-method	coordinates-methods
counts	counts
dbetabinom	dbetabinom
deepSNV	deepSNV-methods
deepSNV,character,character-method	deepSNV-methods
deepSNV,character,matrix-method	deepSNV-methods
deepSNV,deepSNV,missing-method	deepSNV-methods
deepSNV,matrix,character-method	deepSNV-methods
deepSNV,matrix,matrix-method	deepSNV-methods
deepSNV-class	deepSNV-class
estimateDirichlet	estimateDirichlet-methods
estimateDirichlet,deepSNV-method	estimateDirichlet-methods
estimateDirichlet,matrix-method	estimateDirichlet-methods
estimateDispersion	estimateDispersion-methods
estimateDispersion,deepSNV,missing-method	estimateDispersion-methods
estimateDispersion,matrix,matrix-method	estimateDispersion-methods
estimateRho	estimateRho
Extract	Extract-methods
HIVmix	trueSNVs
loadAllData	loadAllData
makePrior	makePrior
manhattanPlot	manhattanPlot
mcChunk	mcChunk
normalize	normalize-methods
normalize,deepSNV,missing-method	normalize-methods
normalize,matrix,matrix-method	normalize-methods
p.combine	p.combine
p.val	p.val-methods
p.val,deepSNV-method	p.val-methods
pbetabinom	pbetabinom
phiX	phiX
pi	pi
plot.deepSNV	plot.deepSNV
qvals2Vcf	qvals2Vcf
RCC	RCC
repeatMask	repeatMask-methods
repeatMask,deepSNV-method	repeatMask-methods
repeatMask,DNAString-method	repeatMask-methods
RF	RF
shearwater	shearwater
show,deepSNV-method	show-deepSNV-method
summary	summary-methods
summary,deepSNV-method	summary-methods
test	test-methods
test,deepSNV-method	test-methods
trueSNVs	trueSNVs
[,deepSNV,ANY,ANY-method	Extract-methods
