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,RiskVariant-method	RiskVariant-class
alt<-	ASEset-class
alt<-,ASEset,ANY-method	ASEset-class
alt<-,RiskVariant,ANY-method	RiskVariant-class
altExist	ASEset-class
altExist,ASEset-method	ASEset-class
annotation-wrappers	annotation-wrappers
annotationBarplot	annotationBarplot
aquals	ASEset-class
aquals,ASEset-method	ASEset-class
aquals<-	ASEset-class
aquals<-,ASEset-method	ASEset-class
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-filters	ASEset-filters
ASEset-gbarplot	ASEset-gbarplot
ASEset-glocationplot	ASEset-glocationplot
ASEset-gviztrack	ASEset-gviztrack
ASEset-locationplot	locationplot
ASEset-scanForHeterozygotes	ASEset-scanForHeterozygotes
ASEset.old	ASEset.old
ASEset.sim	ASEset.sim
ASEsetFromArrays	initialize-ASEset
ASEsetFromBam	ASEsetFromBam
ASEsetFromBam,GRanges-method	ASEsetFromBam
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
basic	RegionSummary-class
basic,RegionSummary-method	RegionSummary-class
binom.test	binom.test
binom.test,ASEset-method	binom.test
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
DetectedAI-plot	DetectedAI-plot
DetectedAI-summary	DetectedAI-summary
DetectedAIFromArray	initialize-DetectedAI
detectedAI_vs_threshold_variable_multigraph_plot	DetectedAI-plot
detectedAI_vs_threshold_variable_multigraph_plot,DetectedAI-method	DetectedAI-plot
detectedAI_vs_threshold_variable_plot	DetectedAI-plot
detectedAI_vs_threshold_variable_plot,DetectedAI-method	DetectedAI-plot
detectedAI_vs_threshold_variable_summary	DetectedAI-summary
detectedAI_vs_threshold_variable_summary,DetectedAI-method	DetectedAI-summary
fraction	ASEset-class
fraction,ASEset-method	ASEset-class
fractionPlotDf	fractionPlotDf
fractionPlotDf,ASEset-method	fractionPlotDf
frequency	ASEset-class
frequency,ASEset-method	ASEset-class
frequency_vs_threshold_variable_multigraph_plot	DetectedAI-plot
frequency_vs_threshold_variable_multigraph_plot,DetectedAI-method	DetectedAI-plot
frequency_vs_threshold_variable_plot	DetectedAI-plot
frequency_vs_threshold_variable_plot,DetectedAI-class	DetectedAI-plot
frequency_vs_threshold_variable_plot,DetectedAI-method	DetectedAI-plot
frequency_vs_threshold_variable_summary	DetectedAI-summary
frequency_vs_threshold_variable_summary,DetectedAI-method	DetectedAI-summary
GAnalysis	initialize-GlobalAnalysis
gba	gba
gba,character-method	gba
gbarplot	ASEset-gbarplot
gbarplot,ASEset-method	ASEset-gbarplot
genomatrix	genomatrix
genotype	ASEset-class
genotype,ASEset-method	ASEset-class
genotype2phase	genotype2phase
genotype2phase,matrix-method	genotype2phase
genotype<-	ASEset-class
genotype<-,ASEset-method	ASEset-class
getAlleleCounts	getAlleleCounts
getAlleleCounts,GAlignmentsList-method	getAlleleCounts
getAlleleQuality	getAlleleQuality
getAlleleQuality,GAlignmentsList-method	getAlleleQuality
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	ASEset-filters
hetFilt,ASEset-method	ASEset-filters
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-RiskVariant	initialize-RiskVariant
legendBarplot	legendBarplot
LinkVariantAlmlof	LinkVariantAlmlof-class
LinkVariantAlmlof-class	LinkVariantAlmlof-class
LinkVariantAlmlof-method	LinkVariantAlmlof-class
LinkVariantAlmlof-plot	LinkVariantAlmlof-plot
locationplot	locationplot
locationplot,ASEset-method	locationplot
lva	lva
lva,array-method	lva
lva,ASEset-method	lva
lva.internal	lva.internal
lva.internal,array-method	lva.internal
makeMaskedFasta	makeMaskedFasta
makeMaskedFasta,character-method	makeMaskedFasta
mapBias	ASEset-class
mapBias,ASEset-method	ASEset-class
mapBias<-	ASEset-class
mapBias<-,ASEset-method	ASEset-class
mapBiasRef	mapBiasRef
mapBiasRef,ASEset-method	mapBiasRef
maternalAllele	ASEset-class
maternalAllele,ASEset-method	ASEset-class
minCountFilt	minCountFilt
minCountFilt,ASEset-method	minCountFilt
minFreqFilt	minFreqFilt
minfreqFilt	minFreqFilt
minFreqFilt,ASEset-method	minFreqFilt
multiAllelicFilt	multiAllelicFilt
multiAllelicFilt,ASEset-method	multiAllelicFilt
paternalAllele	ASEset-class
paternalAllele,ASEset-method	ASEset-class
phase	ASEset-class
phase,ASEset-method	ASEset-class
phase,RiskVariant-method	RiskVariant-class
phase2genotype	phase2genotype
phase2genotype,array-method	phase2genotype
phase<-	ASEset-class
phase<-,ASEset-method	ASEset-class
phase<-,RiskVariant-method	RiskVariant-class
phaseArray2phaseMatrix	phaseArray2phaseMatrix
phaseArray2phaseMatrix,array-method	phaseArray2phaseMatrix
phaseMatrix2Array	phaseMatrix2Array
phaseMatrix2Array,matrix-method	phaseMatrix2Array
plot	LinkVariantAlmlof-plot
plot,LinkVariantAlmlof,ANY-method	LinkVariantAlmlof-plot
plot,LinkVariantAlmlof-method	LinkVariantAlmlof-plot
pvalue	LinkVariantAlmlof-class
pvalue,LinkVariantAlmlof-method	LinkVariantAlmlof-class
randomRef	randomRef
randomRef,ASEset-method	randomRef
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,RiskVariant-method	RiskVariant-class
ref<-	ASEset-class
ref<-,ASEset,ANY-method	ASEset-class
ref<-,RiskVariant,ANY-method	RiskVariant-class
refAllele	refAllele
refAllele,ASEset-method	refAllele
referenceFrequency	DetectedAI-class
referenceFrequency,DetectedAI-method	DetectedAI-class
reference_frequency_density_vs_threshold_variable_multigraph_plot	DetectedAI-plot
reference_frequency_density_vs_threshold_variable_multigraph_plot,DetectedAI-method	DetectedAI-plot
reference_frequency_density_vs_threshold_variable_plot	DetectedAI-plot
reference_frequency_density_vs_threshold_variable_plot,DetectedAI-method	DetectedAI-plot
refExist	ASEset-class
refExist,ASEset-method	ASEset-class
RegionSummary	RegionSummary-class
regionSummary	regionSummary
regionSummary,ASEset-method	regionSummary
regionSummary,numeric-method	regionSummary
RegionSummary-class	RegionSummary-class
RegionSummary-method	RegionSummary-class
RiskVariant	RiskVariant-class
RiskVariant-class	RiskVariant-class
RiskVariant-method	RiskVariant-class
RiskVariantFromGRangesAndPhaseArray	initialize-RiskVariant
scanForHeterozygotes	ASEset-scanForHeterozygotes
scanForHeterozygotes,ASEset-method	ASEset-scanForHeterozygotes
scanForHeterozygotes,GAlignmentsList-method	ASEset-scanForHeterozygotes
scanForHeterozygotes.old	scanForHeterozygotes-old
sumnames	RegionSummary-class
sumnames,RegionSummary-method	RegionSummary-class
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
usedSNPs_vs_threshold_variable_summary	DetectedAI-summary
usedSNPs_vs_threshold_variable_summary,DetectedAI-method	DetectedAI-summary
