AllelicImbalance-package	AllelicImbalance-package
alleleCounts	ASEset-class
alleleCounts,ASEset-method	ASEset-class
alleleCounts<-	ASEset-class
alleleCounts<-,ASEset-method	ASEset-class
AllelicImbalance	AllelicImbalance-package
alt	ASEset-class
alt,ASEset-method	ASEset-class
alt<-	ASEset-class
alt<-,ASEset,ANY-method	ASEset-class
annotation-wrappers	annotation-wrappers
annotationBarplot	annotationBarplot
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-gbarplot	ASEset-gbarplot
ASEset-glocationplot	ASEset-glocationplot
ASEset-gviztrack	ASEset-gviztrack
ASEset-locationplot	locationplot
ASEset-scanForHeterozygotes	ASEset-scanForHeterozygotes
ASEset.sim	ASEset.sim
ASEsetFromArrays	initialize-ASEset
ASEsetFromBam	ASEsetFromBam
ASEsetFromBam,GRanges-method	ASEsetFromBam
ASEsetFromCountList	initialize-ASEset
BamList	getAlleleCounts
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
countAllelesFromBam	countAllelesFromBam
countAllelesFromBam,GRanges-method	countAllelesFromBam
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
coverageMatrixListFromGAL,GAlignmentsList-method	coverageMatrixListFromGAL
decorateWithExons	decorateWithExons
decorateWithGenes	decorateWithGenes
defaultMapBias	defaultMapBias
defaultMapBias,ASEset-method	defaultMapBias
defaultPhase	defaultPhase
defaultPhase,numeric-method	defaultPhase
detectAI	detectAI
detectAI,ASEset-method	detectAI
DetectedAI	DetectedAI-class
DetectedAI-class	DetectedAI-class
DetectedAI-method	DetectedAI-class
DetectedAIFromArray	initialize-DetectedAI
fraction	ASEset-class
fraction,ASEset-method	ASEset-class
fractionPlotDf	fractionPlotDf
fractionPlotDf,ASEset-method	fractionPlotDf
frequency	ASEset-class
frequency,ASEset-method	ASEset-class
frequency,ReferenceBias-method	ReferenceBias-class
GAnalysis	initialize-GlobalAnalysis
gba	gba
gba,character-method	gba
gbarplot	ASEset-gbarplot
gbarplot,ASEset-method	ASEset-gbarplot
genofilters	genofilters
genotype	ASEset-class
genotype,ASEset-method	ASEset-class
genotype<-	ASEset-class
genotype<-,ASEset-method	ASEset-class
getAlleleCounts	getAlleleCounts
getAlleleCounts,GAlignmentsList-method	getAlleleCounts
getAnnotationDataFrame	annotation-wrappers
getAreaFromGeneNames	getAreaFromGeneNames
getAreaFromGeneNames,character-method	getAreaFromGeneNames
getCDSFromAnnotation	annotation-wrappers
getCDSVector	annotation-wrappers
getDefaultMapBiasExpMean	getDefaultMapBiasExpMean
getDefaultMapBiasExpMean,ANY-method	getDefaultMapBiasExpMean
getDefaultMapBiasExpMean,list-method	getDefaultMapBiasExpMean
getDefaultMapBiasExpMean3D	getDefaultMapBiasExpMean
getDefaultMapBiasExpMean3D,ANY-method	getDefaultMapBiasExpMean
getExonsFromAnnotation	annotation-wrappers
getExonsVector	annotation-wrappers
getGenesFromAnnotation	annotation-wrappers
getGenesVector	annotation-wrappers
getSnpIdFromLocation	getSnpIdFromLocation
getSnpIdFromLocation,GRanges-method	getSnpIdFromLocation
getTranscriptsFromAnnotation	annotation-wrappers
getTranscriptsVector	annotation-wrappers
GlobalAnalysis	GlobalAnalysis-class
GlobalAnalysis-class	GlobalAnalysis-class
GlobalAnalysis-method	GlobalAnalysis-class
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
impBamGAL,character-method	import-bam
impBamGRL	import-bam-2
impBamGRL.old	import-bam-2
impBcfGR	import-bcf
impBcfGR,character-method	import-bcf
impBcfGRL	import-bcf
impBcfGRL,character-method	import-bcf
implodeList.old	implodeList-old
import-bam	import-bam
import-bam-2	import-bam-2
import-bcf	import-bcf
inferAlleles	inferAlleles
inferAlleles,ASEset-method	inferAlleles
inferAltAllele	inferAltAllele
inferAltAllele,ASEset-method	inferAltAllele
inferGenotypes	inferGenotypes
inferGenotypes,ASEset-method	inferGenotypes
initialize-ASEset	initialize-ASEset
initialize-DetectedAI	initialize-DetectedAI
initialize-GlobalAnalysis	initialize-GlobalAnalysis
initialize-ReferenceBias	initialize-ReferenceBias
legendBarplot	legendBarplot
locationplot	locationplot
locationplot,ASEset-method	locationplot
makeMaskedFasta	makeMaskedFasta
makeMaskedFasta,character-method	makeMaskedFasta
mapBias	ASEset-class
mapBias,ASEset-method	ASEset-class
mapBiasRef	mapBiasRef
mapBiasRef,ASEset-method	mapBiasRef
phase	ASEset-class
phase,ASEset-method	ASEset-class
phase<-	ASEset-class
phase<-,ASEset-method	ASEset-class
phaseArray2Matrix	phaseArray2Matrix
phaseArray2Matrix,array-method	phaseArray2Matrix
phaseMatrix2Array	phaseMatrix2Array
phaseMatrix2Array,matrix-method	phaseMatrix2Array
randomRef	randomRef
randomRef,ASEset-method	randomRef
RBias	initialize-ReferenceBias
reads	reads
realCigarPosition	cigar-utilities
realCigarPosition.old	cigar-utilities
realCigarPositions	cigar-utilities
realCigarPositions.old	cigar-utilities
realCigarPositionsList	cigar-utilities
realCigarPositionsList.old	cigar-utilities
ref	ASEset-class
ref,ASEset-method	ASEset-class
ref<-	ASEset-class
ref<-,ASEset,ANY-method	ASEset-class
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
referenceFrequency	DetectedAI-class
referenceFrequency,DetectedAI-method	DetectedAI-class
refFraction	refFraction
refFraction,ASEset-method	refFraction
regionSummary	regionSummary
regionSummary,ASEset-method	regionSummary
regionSummary,numeric-method	regionSummary
scanForHeterozygotes	ASEset-scanForHeterozygotes
scanForHeterozygotes,ASEset-method	ASEset-scanForHeterozygotes
scanForHeterozygotes,GAlignmentsList-method	ASEset-scanForHeterozygotes
scanForHeterozygotes.old	scanForHeterozygotes-old
show,ReferenceBias-method	ReferenceBias-show
thresholdCountSample	DetectedAI-class
thresholdCountSample,DetectedAI-method	DetectedAI-class
thresholdDeltaFrequency	DetectedAI-class
thresholdDeltaFrequency,DetectedAI-method	DetectedAI-class
thresholdFrequency	DetectedAI-class
thresholdFrequency,DetectedAI-method	DetectedAI-class
thresholdPvalue	DetectedAI-class
thresholdPvalue,DetectedAI-method	DetectedAI-class
