ASEset-barplot          barplot ASEset objects
ASEset-class            ASEset objects
ASEset-filters          genotype filter methods
ASEset-gbarplot         gbarplot ASEset objects
ASEset-glocationplot    glocationplot ASEset objects
ASEset-gviztrack        ASEset-gviztrack ASEset objects
ASEset-locationplot     locationplot ASEset objects
ASEset-scanForHeterozygotes
                        scanForHeterozygotes
ASEset.old              ASEset.old object
ASEset.sim              ASEset.sim object
ASEsetFromBam           ASEset from bam file
AllelicImbalance-package
                        A package meant to provide all basic functions
                        for high-throughput allele specific expression
                        analysis
DetectedAI-class        DetectedAI class
DetectedAI-plot         DetectedAI plot
DetectedAI-summary      DetectedAI summary
GRvariants              GRvariants object
GlobalAnalysis-class    GlobalAnalysis class
LinkVariantAlmlof-class
                        LinkVariantAlmlof class
LinkVariantAlmlof-plot
                        plot LinkVariantAlmlof objects
RegionSummary-class     RegionSummary class
RiskVariant-class       RiskVariant class
annotation-wrappers     AnnotationDb wrappers
annotationBarplot       add annotation to AllelicImbalance barplot
barplot-lattice-support
                        lattice barplot inner functions for ASEset
                        objects
binom.test              binomial test
chisq.test              chi-square test
countAllelesFromBam     alleleCounts from bam file
coverageMatrixListFromGAL
                        coverage matrix of GAlignmentsList
defaultMapBias          Generate default mapbias from genotype
defaultPhase            defaultPhase
detectAI                detectAI
fractionPlotDf          Plot Dataframe
gba                     global analysis wrapper
genomatrix              genomatrix object
genotype2phase          genotype2phase
getAlleleCounts         snp count data
getAlleleQuality        snp quality data
getAreaFromGeneNames    Get Gene Area
getDefaultMapBiasExpMean
                        Map Bias
getSnpIdFromLocation    Get rsIDs from locations of SNP
histplot                histogram plots
implodeList.old         implode list of arguments into environment
import-bam              Import Bam
import-bam-2            Import Bam-2
import-bcf              Import Bcf Selection
inferAlleles            inference of SNPs of ASEset
inferAltAllele          inferAltAllele
inferGenotypes          infererence of genotypes from ASEset count data
initialize-ASEset       Initialize ASEset
initialize-DetectedAI   Initialize DetectedAI
initialize-GlobalAnalysis
                        Initialize GlobalAnalysis
initialize-RiskVariant
                        Initialize RiskVariant
legendBarplot           add legend to AllelicImbalance barplot
lva                     lva
lva.internal            lva.internal
makeMaskedFasta         makes masked fasta reference
mapBiasRef              mapBias for reference allele
minCountFilt            minCountFilt methods
minFreqFilt             minFreqFilt methods
multiAllelicFilt        multi-allelic filter methods
phase2genotype          phase2genotype
phaseArray2phaseMatrix
                        phaseArray2phaseMatrix
phaseMatrix2Array       phaseMatrix2Array
randomRef               Random ref allele from genotype
reads                   reads object
refAllele               Reference allele
regionSummary           regionSummary
scanForHeterozygotes.old
                        scanForHeterozygotes-old
