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| AllelicImbalance-package | A package meant to provide all basic functions for high-throughput allele specific expression analysis |
| alleleCounts | ASEset objects |
| alleleCounts-method | ASEset objects |
| alleleCounts<- | ASEset objects |
| alleleCounts<--method | ASEset objects |
| AllelicImbalance | A package meant to provide all basic functions for high-throughput allele specific expression analysis |
| annotation-wrappers | AnnotationDb wrappers |
| arank | ASEset objects |
| arank-method | ASEset objects |
| ASEDAnnotationTrack | ASEset-gviztrack ASEset objects |
| ASEDAnnotationTrack-method | ASEset-gviztrack ASEset objects |
| ASEset | ASEset objects |
| 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 |
| ASEsetFromCountList | Initialize ASEset |
| barplot | barplot ASEset objects |
| barplot-lattice-support | lattice barplot inner functions for ASEset objects |
| barplot-method | barplot ASEset objects |
| barplotLatticeCounts | lattice barplot inner functions for ASEset objects |
| barplotLatticeFraction | lattice barplot inner functions for ASEset objects |
| binom.test | binomial test |
| binom.test-method | binomial test |
| boxplot | boxplots |
| boxplot-method | boxplots |
| chisq.test | chi-square test |
| chisq.test-method | chi-square test |
| countsPerSample | ASEset objects |
| countsPerSample-method | ASEset objects |
| countsPerSnp | ASEset objects |
| countsPerSnp-method | ASEset objects |
| CoverageDataTrack | ASEset-gviztrack ASEset objects |
| CoverageDataTrack-method | ASEset-gviztrack ASEset objects |
| coverageMatrixListFromGAL | coverage matrix of GAlignmentsList |
| defaultMapBias | Generate default mapbias from genotype |
| defaultMapBias-method | Generate default mapbias from genotype |
| detectAI | detectAI |
| detectAI-method | detectAI |
| fraction | ASEset objects |
| fraction-method | ASEset objects |
| frequency | ASEset objects |
| frequency-method | ASEset objects |
| frequency-method | ReferenceBias class |
| genofilters | genotype filter methods |
| genotype | ASEset objects |
| genotype-method | ASEset objects |
| genotype<- | ASEset objects |
| genotype<--method | ASEset objects |
| getAlleleCounts | snp count data |
| getAnnotationDataFrame | AnnotationDb wrappers |
| getAreaFromGeneNames | Get Gene Area |
| getCDSFromAnnotation | AnnotationDb wrappers |
| getCDSVector | AnnotationDb wrappers |
| getDefaultMapBiasExpMean | Map Bias |
| getDefaultMapBiasExpMean3D | Map Bias |
| getExonsFromAnnotation | AnnotationDb wrappers |
| getExonsVector | AnnotationDb wrappers |
| getGenesFromAnnotation | AnnotationDb wrappers |
| getGenesVector | AnnotationDb wrappers |
| getSnpIdFromLocation | Get rsIDs from locations of SNP |
| getTranscriptsFromAnnotation | AnnotationDb wrappers |
| getTranscriptsVector | AnnotationDb wrappers |
| glocationplot | glocationplot ASEset objects |
| glocationplot-method | glocationplot ASEset objects |
| GRvariants | GRvariants object |
| hetFilt | genotype filter methods |
| hetFilt-method | genotype filter methods |
| hetPerSample | ReferenceBias class |
| hetPerSample-method | ReferenceBias class |
| hetPerSnp | ReferenceBias class |
| hetPerSnp-method | ReferenceBias class |
| hist | histogram plots |
| hist-method | histogram plots |
| histplot | histogram plots |
| impBamGAL | Import Bam |
| impBamGRL | Import Bam |
| impBcfGR | Import Bcf Selection |
| impBcfGRL | Import Bcf Selection |
| implodeList | implode list of arguments into environment |
| import-bam | Import Bam |
| import-bcf | Import Bcf Selection |
| inferAlleles | inference of SNPs of ASEset |
| inferAlleles-method | inference of SNPs of ASEset |
| inferGenotypes | infererence of genotypes from ASEset count data |
| inferGenotypes-method | infererence of genotypes from ASEset count data |
| initialize-ASEset | Initialize ASEset |
| initialize-ReferenceBias | Initialize ReferenceBias |
| lbarplot | lbarplot ASEset objects |
| lbarplot-method | lbarplot ASEset objects |
| locationplot | locationplot ASEset objects |
| locationplot-method | locationplot ASEset objects |
| mapBias | ASEset objects |
| mapBias-method | ASEset objects |
| RBias | Initialize ReferenceBias |
| reads | reads object |
| refAllele | Reference allele |
| refAllele-method | Reference allele |
| refbiasByAnnotation | ReferenceBias class |
| refbiasByAnnotation-method | ReferenceBias class |
| ReferenceBias | ReferenceBias class |
| ReferenceBias-class | ReferenceBias class |
| ReferenceBias-method | ReferenceBias class |
| ReferenceBias-show | genotype filter methods |
| ReferenceBias-show-method | genotype filter methods |
| refFraction | reference fraction |
| refFraction-method | reference fraction |
| scanForHeterozygotes | scanForHeterozygotes |
| show-method | genotype filter methods |