ASEset-barplot          barplot ASEset objects
ASEset-class            ASEset objects
ASEset-glocationplot    glocationplot ASEset objects
ASEset-gviztrack        ASEset-gviztrack ASEset objects
ASEset-lbarplot         lbarplot ASEset objects
ASEset-locationplot     locationplot ASEset objects
ASEset.sim              ASEset.sim object
AllelicImbalance-package
                        A package meant to provide all basic functions
                        for high-throughput allele specific expression
                        analysis
GRvariants              GRvariants object
ReferenceBias-class     ReferenceBias class
ReferenceBias-show      genotype filter methods
annotation-wrappers     AnnotationDb wrappers
barplot-lattice-support
                        lattice barplot inner functions for ASEset
                        objects
binom.test              binomial test
boxplot                 boxplots
chisq.test              chi-square test
coverageMatrixListFromGAL
                        coverage matrix of GAlignmentsList
defaultMapBias          Generate default mapbias from genotype
detectAI                detectAI
genofilters             genotype filter methods
getAlleleCounts         snp count data
getAreaFromGeneNames    Get Gene Area
getDefaultMapBiasExpMean
                        Map Bias
getSnpIdFromLocation    Get rsIDs from locations of SNP
histplot                histogram plots
implodeList             implode list of arguments into environment
import-bam              Import Bam
import-bcf              Import Bcf Selection
inferAlleles            inference of SNPs of ASEset
inferGenotypes          infererence of genotypes from ASEset count data
initialize-ASEset       Initialize ASEset
initialize-ReferenceBias
                        Initialize ReferenceBias
reads                   reads object
refAllele               Reference allele
refFraction             reference fraction
scanForHeterozygotes    scanForHeterozygotes
