AllelicImbalance-package	AllelicImbalance-package
alleleCounts	ASEset-class
alleleCounts,ASEset-method	ASEset-class
alleleCounts<-	ASEset-class
alleleCounts<-,ASEset-method	ASEset-class
AllelicImbalance	AllelicImbalance-package
annotation-wrappers	annotation-wrappers
arank	ASEset-class
arank,ASEset-method	ASEset-class
ASEDAnnotationTrack	ASEset-gviztrack
ASEDAnnotationTrack,ASEset-method	ASEset-gviztrack
ASEset	ASEset-class
ASEset-barplot	ASEset-barplot
ASEset-class	ASEset-class
ASEset-glocationplot	ASEset-glocationplot
ASEset-gviztrack	ASEset-gviztrack
ASEset-lbarplot	ASEset-lbarplot
ASEset-locationplot	ASEset-locationplot
ASEset.sim	ASEset.sim
ASEsetFromCountList	initialize-ASEset
barplot	ASEset-barplot
barplot,ASEset-method	ASEset-barplot
barplot-lattice-support	barplot-lattice-support
barplotLatticeCounts	barplot-lattice-support
barplotLatticeFraction	barplot-lattice-support
binom.test	binom.test
binom.test,ASEset-method	binom.test
boxplot	boxplot
boxplot,ReferenceBias-method	boxplot
chisq.test	chisq.test
chisq.test,ASEset-method	chisq.test
cigar-utilities	cigar-utilities
countsPerSample	ASEset-class
countsPerSample,ASEset-method	ASEset-class
countsPerSnp	ASEset-class
countsPerSnp,ASEset-method	ASEset-class
CoverageDataTrack	ASEset-gviztrack
CoverageDataTrack,ASEset-method	ASEset-gviztrack
coverageMatrixListFromGAL	coverageMatrixListFromGAL
decorateWithExons	decorateWithExons
decorateWithGenes	decorateWithGenes
defaultMapBias	defaultMapBias
defaultMapBias,ASEset-method	defaultMapBias
detectAI	detectAI
detectAI,ASEset-method	detectAI
fraction	ASEset-class
fraction,ASEset-method	ASEset-class
frequency	ASEset-class
frequency,ASEset-method	ASEset-class
frequency,ReferenceBias-method	ReferenceBias-class
genofilters	genofilters
genotype	ASEset-class
genotype,ASEset-method	ASEset-class
genotype<-	ASEset-class
genotype<-,ASEset-method	ASEset-class
getAlleleCounts	getAlleleCounts
getAnnotationDataFrame	annotation-wrappers
getAreaFromGeneNames	getAreaFromGeneNames
getCDSFromAnnotation	annotation-wrappers
getCDSVector	annotation-wrappers
getDefaultMapBiasExpMean	getDefaultMapBiasExpMean
getDefaultMapBiasExpMean3D	getDefaultMapBiasExpMean
getExonsFromAnnotation	annotation-wrappers
getExonsVector	annotation-wrappers
getGenesFromAnnotation	annotation-wrappers
getGenesVector	annotation-wrappers
getSnpIdFromLocation	getSnpIdFromLocation
getTranscriptsFromAnnotation	annotation-wrappers
getTranscriptsVector	annotation-wrappers
glocationplot	ASEset-glocationplot
glocationplot,ASEset-method	ASEset-glocationplot
GRvariants	GRvariants
hetFilt	genofilters
hetFilt,ASEset-method	genofilters
hetPerSample	ReferenceBias-class
hetPerSample,ReferenceBias-method	ReferenceBias-class
hetPerSnp	ReferenceBias-class
hetPerSnp,ReferenceBias-method	ReferenceBias-class
hist	histplot
hist,ASEset-method	histplot
hist,ReferenceBias-method	histplot
histplot	histplot
impBamGAL	import-bam
impBamGRL	import-bam
impBcfGR	import-bcf
impBcfGRL	import-bcf
implodeList	implodeList
import-bam	import-bam
import-bcf	import-bcf
inferAlleles	inferAlleles
inferAlleles,ASEset-method	inferAlleles
inferGenotypes	inferGenotypes
inferGenotypes,ASEset-method	inferGenotypes
initialize-ASEset	initialize-ASEset
initialize-ReferenceBias	initialize-ReferenceBias
lbarplot	ASEset-lbarplot
lbarplot,ASEset-method	ASEset-lbarplot
locationplot	ASEset-locationplot
locationplot,ASEset-method	ASEset-locationplot
mapBias	ASEset-class
mapBias,ASEset-method	ASEset-class
RBias	initialize-ReferenceBias
reads	reads
realCigarPosition	cigar-utilities
realCigarPositions	cigar-utilities
realCigarPositionsList	cigar-utilities
refAllele	refAllele
refAllele,ASEset-method	refAllele
refbiasByAnnotation	ReferenceBias-class
refbiasByAnnotation,ReferenceBias-method	ReferenceBias-class
ReferenceBias	ReferenceBias-class
ReferenceBias-class	ReferenceBias-class
ReferenceBias-method	ReferenceBias-class
ReferenceBias-show	ReferenceBias-show
ReferenceBias-show,ReferenceBias-method	ReferenceBias-show
refFraction	refFraction
refFraction,ASEset-method	refFraction
scanForHeterozygotes	scanForHeterozygotes
show,ReferenceBias-method	ReferenceBias-show
